From 14f0ab46c45f3dd61005a6bdcfcc5f52e824f0e3 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 8 Oct 2024 12:32:00 +0000 Subject: [PATCH 01/35] Template update for nf-core/tools version 3.0.0 --- .editorconfig | 4 + .github/CONTRIBUTING.md | 10 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 23 +- .github/workflows/ci.yml | 17 +- .github/workflows/download_pipeline.yml | 53 ++- .github/workflows/linting.yml | 23 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 43 ++ .gitpod.yml | 7 +- .nf-core.yml | 29 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + CHANGELOG.md | 2 +- CITATIONS.md | 4 +- README.md | 5 +- assets/multiqc_config.yml | 4 +- assets/schema_input.json | 2 +- conf/base.config | 34 +- conf/igenomes_ignored.config | 9 + conf/modules.config | 1 - conf/test.config | 13 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 11 +- docs/usage.md | 12 +- main.nf | 10 +- modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/fastqc/meta.yml | 57 +-- modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 14 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 20 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 148 ++++--- nextflow_schema.json | 85 +--- .../utils_nfcore_rnaseq_pipeline/main.nf | 56 +-- .../nf-core/utils_nextflow_pipeline/main.nf | 24 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 45 ++- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ---------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/rnaseq.nf | 23 +- 57 files changed, 1220 insertions(+), 810 deletions(-) create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 conf/igenomes_ignored.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 72dda289a..e10588156 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,6 +11,7 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 + # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -25,9 +26,12 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset + + [/assets/email*] indent_size = unset + # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index d784a8bbc..9bd7d6166 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/rnaseq, the standard workflow is as 1. Check that there isn't already an issue about your idea in the [nf-core/rnaseq issues](https://github.com/nf-core/rnaseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/rnaseq repository](https://github.com/nf-core/rnaseq) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 5ed2fd931..3473f145d 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 37d6f369b..e56f84788 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,33 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/rnaseq' + if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0c9f57c95..28e81784a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,6 +7,7 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false @@ -24,7 +25,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" steps: - name: Check out pipeline code @@ -38,9 +39,21 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data + - name: Run pipeline with test data (docker) # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + + - name: Run pipeline with test data (singularity) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results + if: "${{ github.base_ref == 'master' }}" + + - name: Run pipeline with test data (conda) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results + if: "${{ github.base_ref == 'master' }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d6442..713dc3e73 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -54,33 +56,64 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe880..b882838af 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,32 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f5..42e519bfa 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf72..c6ba35df4 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 000000000..9dea41f0d --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,43 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Read template version from .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: pip list --outdated | grep nf-core + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + ## :warning: Newer version of the nf-core template is available. + + Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + Please update your pipeline to the latest version. + + For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitpod.yml b/.gitpod.yml index 105a1821a..461186376 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,14 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a77f..733c3bfd6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,29 @@ +bump_version: null +lint: + actions_ci: false + files_exist: + - conf/modules.config + files_unchanged: + - assets/email_template.html + - assets/email_template.txt + - .gitignore + modules_config: false + multiqc_config: false + nextflow_config: + - config_defaults: + - params.ribo_database_manifest +nf_core_version: 3.0.0 +org_path: null repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n" + description: RNA sequencing analysis pipeline for gene/isoform quantification and + extensive quality control. + force: false + is_nfcore: true + name: rnaseq + org: nf-core + outdir: . + skip_features: null + version: 3.16.0 +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dcd..9e9f0e1c4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/.prettierignore b/.prettierignore index 437d763d0..610e50692 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,3 +1,4 @@ + email_template.html adaptivecard.json slackreport.json diff --git a/CHANGELOG.md b/CHANGELOG.md index ab4540c69..38767108a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.15.0dev - [date] +## v3.16.0 - [date] Initial release of nf-core/rnaseq, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index cae7ea444..deb2f0f58 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index d067db739..d0e01a60a 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -67,8 +67,7 @@ nextflow run nf-core/rnaseq \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters). diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 2bb92717b..281e49ad5 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnaseq + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnaseq-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index cba734bf1..e6c6ae775 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/rnaseq/master/assets/schema_input.json", "title": "nf-core/rnaseq pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index 62976e730..92ebdab4d 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,9 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +27,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 000000000..b4034d824 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b6e..d266a387f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,7 +21,6 @@ process { withName: FASTQC { ext.args = '--quiet' } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index d23e84f89..6efe32449 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index fdd9683f0..bc029f00d 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline + - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -29,16 +30,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index 8ab7744b6..248c0aa35 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/rnaseq -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index b36a906c7..3bb15e190 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,7 +18,6 @@ nextflow.enable.dsl = 2 include { RNASEQ } from './workflows/rnaseq' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnaseq_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rnaseq_pipeline' - include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_rnaseq_pipeline' /* @@ -56,10 +53,8 @@ workflow NFCORE_RNASEQ { RNASEQ ( samplesheet ) - emit: multiqc_report = RNASEQ.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,27 +65,24 @@ workflow NFCORE_RNASEQ { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // NFCORE_RNASEQ ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index 088b5058a..874901fa9 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a9..691d4c763 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c862..d8989f481 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e06..4827da7af 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d9..e9d79a074 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c3115..d5db3092f 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67e..f1cd99b07 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f9..b9ccebdbb 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35e..b16c18792 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242ef..33316a7dd 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd8029..b779e4692 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 000000000..c537a6a3e --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index f1f5b4a38..ae8f8095b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,6 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -33,48 +32,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true + } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/rnaseq custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/rnaseq.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/rnaseq profiles: ${params.custom_config_base}/pipeline/rnaseq.config") -} profiles { debug { dumpHashes = true @@ -89,7 +66,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -178,25 +155,23 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/rnaseq custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null" +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -208,8 +183,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -238,43 +220,47 @@ manifest { homePage = 'https://github.com/nf-core/rnaseq' description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '3.15.0dev' + nextflowVersion = '!>=24.04.2' + version = '3.16.0' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + diff --git a/nextflow_schema.json b/nextflow_schema.json index 13656263e..c1004ac3d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/rnaseq/master/nextflow_schema.json", "title": "nf-core/rnaseq pipeline parameters", "description": "RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -71,6 +71,14 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -122,41 +130,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +137,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -245,27 +212,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -278,19 +224,16 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index a20c37b15..f68415fd4 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -8,17 +8,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* ======================================================================================== @@ -30,7 +27,6 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -51,20 +47,16 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) + // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) + // // Check config provided to the pipeline @@ -80,8 +72,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -91,8 +84,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -117,13 +110,13 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -131,11 +124,18 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -165,7 +165,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -197,7 +197,6 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // @@ -239,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +262,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f6..28e32b200 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,10 +2,6 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) @@ -102,14 +98,16 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + + required_channels_in_order.eachWithIndex { channel, index -> + if (index < required_channels_in_order.size() - 1) { + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + } } if (channels_missing | channel_priority_violation) { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf6..a09572e5b 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c392..cbd8495bb 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,9 +2,6 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE { // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + @@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") + def manifest_doi = workflow.manifest.doi.tokenize(",") // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + @@ -84,7 +83,7 @@ def workflowCitation() { // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +101,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -124,7 +123,7 @@ def workflowVersionToYAML() { def softwareVersionsToYAML(ch_versions) { return ch_versions .unique() - .map { processVersionsFromYAML(it) } + .map { version -> processVersionsFromYAML(version) } .unique() .mix(Channel.of(workflowVersionToYAML())) } @@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { + summary_params.keySet().each { group -> def group_params = summary_params.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

    $group

    \n" summary_section += "
    \n" - for (param in group_params.keySet()) { + group_params.keySet().sort().each { param -> summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" } summary_section += "
    \n" } } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" @@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi } def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } @@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" @@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 000000000..4994303ea --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 000000000..f7d9f0288 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 000000000..842dc432a --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 000000000..0907ac58f --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c93..331e0d2f4 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65d1..000000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04f..000000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f2..000000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff4..000000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index d7cc4e3b2..eb3516ac4 100644 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -3,10 +3,9 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnaseq_pipeline' @@ -21,12 +20,10 @@ workflow RNASEQ { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // // MODULE: Run FastQC // @@ -42,11 +39,12 @@ workflow RNASEQ { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -59,18 +57,19 @@ workflow RNASEQ { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +82,14 @@ workflow RNASEQ { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From db6dfd017651420dcb8338b1b72e7d2d864fd755 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 9 Oct 2024 11:09:00 +0000 Subject: [PATCH 02/35] Template update for nf-core/tools version 3.0.1 --- .editorconfig | 4 - .github/CONTRIBUTING.md | 2 +- .github/workflows/awsfulltest.yml | 6 +- .github/workflows/linting.yml | 4 +- .nf-core.yml | 4 +- .prettierignore | 1 - CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 +- docs/output.md | 1 - modules.json | 6 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 26 +- nextflow.config | 10 +- .../utils_nfcore_rnaseq_pipeline/main.nf | 12 +- .../nf-core/utils_nextflow_pipeline/main.nf | 46 ++- .../nf-core/utils_nfcore_pipeline/main.nf | 279 ++++++++++-------- 17 files changed, 214 insertions(+), 199 deletions(-) diff --git a/.editorconfig b/.editorconfig index e10588156..72dda289a 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,7 +11,6 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 - # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -26,12 +25,9 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset - - [/assets/email*] indent_size = unset - # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 9bd7d6166..f2e9f3318 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e56f84788..0163d6fb6 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,16 +14,18 @@ on: jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - uses: octokit/request-action@v2.x id: check_approvals with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables + if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b882838af..a502573c5 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -42,10 +42,10 @@ jobs: architecture: "x64" - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: pietrobolcato/action-read-yaml@1.1.0 id: read_yml with: - config: ${{ github.workspace }}/.nf-core.yaml + config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies run: | diff --git a/.nf-core.yml b/.nf-core.yml index 733c3bfd6..15806017b 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -12,7 +12,7 @@ lint: nextflow_config: - config_defaults: - params.ribo_database_manifest -nf_core_version: 3.0.0 +nf_core_version: 3.0.1 org_path: null repository_type: pipeline template: @@ -25,5 +25,5 @@ template: org: nf-core outdir: . skip_features: null - version: 3.16.0 + version: 3.17.0dev update: null diff --git a/.prettierignore b/.prettierignore index 610e50692..437d763d0 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,4 +1,3 @@ - email_template.html adaptivecard.json slackreport.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 38767108a..b5f7885db 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.16.0 - [date] +## v3.17.0dev - [date] Initial release of nf-core/rnaseq, created with the [nf-core](https://nf-co.re/) template. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 281e49ad5..2bb92717b 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnaseq + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnaseq-methods-description": order: -1000 diff --git a/docs/output.md b/docs/output.md index bc029f00d..38843ffc2 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,7 +14,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC diff --git a/modules.json b/modules.json index 874901fa9..76a08c3e6 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", + "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", + "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b07..6f5b867b7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index b9ccebdbb..9724d2f34 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index b779e4692..2fcbb5ff7 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-10-02T17:52:09.185842" } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index ae8f8095b..eba3d3ed5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,10 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false + // MultiQC options multiqc_config = null multiqc_title = null @@ -36,6 +38,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + // Config options config_profile_name = null config_profile_description = null @@ -44,9 +47,9 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null + // Schema validation default options validate_params = true - } // Load base.config by default for all pipelines @@ -161,6 +164,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load nf-core/rnaseq custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null" + // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers @@ -172,6 +176,7 @@ charliecloud.registry = 'quay.io' // Load igenomes.config if required includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -221,7 +226,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.16.0' + version = '3.17.0dev' doi = '' } @@ -263,4 +268,3 @@ validation { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index f68415fd4..9021958bf 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -18,9 +18,9 @@ include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { @@ -99,9 +99,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -147,9 +147,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 28e32b200..2b0dc67a6 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -72,11 +71,11 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() @@ -91,9 +90,14 @@ def checkCondaChannels() { try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present @@ -106,19 +110,13 @@ def checkCondaChannels() { required_channels_in_order.eachWithIndex { channel, index -> if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) } } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn( + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index cbd8495bb..b78273ca4 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE { def checkConfigProvided() { def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -49,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -70,13 +68,7 @@ def workflowCitation() { manifest_doi.each { doi_ref -> temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // @@ -102,7 +94,7 @@ def getWorkflowVersion() { // def processVersionsFromYAML(yaml_file) { def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -121,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { version -> processVersionsFromYAML(version) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - summary_params.keySet().each { group -> - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - group_params.keySet().sort().each { param -> - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() @@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) { def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } From 0dbd32a371ac42495c216948162dcd9e4105aa8c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 15:56:23 +0200 Subject: [PATCH 03/35] fix merge conflicts --- modules.json | 8 ++--- modules/nf-core/multiqc/tests/main.nf.test | 2 -- .../nf-core/multiqc/tests/main.nf.test.snap | 35 +------------------ .../nf-core/utils_nextflow_pipeline/main.nf | 8 ++--- .../nf-core/utils_nfcore_pipeline/main.nf | 26 +++----------- workflows/rnaseq/main.nf | 6 ++-- 6 files changed, 16 insertions(+), 69 deletions(-) diff --git a/modules.json b/modules.json index 4b08a9b1c..02127acb3 100644 --- a/modules.json +++ b/modules.json @@ -53,7 +53,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "fq/subsample": { @@ -104,7 +104,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", "installed_by": ["modules"] }, "picard/markduplicates": { @@ -352,12 +352,12 @@ }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", + "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", + "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 1a6b81434..f815b6de3 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -5,8 +5,6 @@ nextflow_process { process "MULTIQC" config "./nextflow.config" - config "./nextflow.config" - test("sarscov2 single-end [fastqc]") { when { diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2a2c748cf..2fcbb5ff7 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,7 +2,6 @@ "multiqc_versions_single": { "content": [ [ -<<<<<<< HEAD "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], @@ -11,16 +10,6 @@ "nextflow": "24.04.4" }, "timestamp": "2024-10-02T17:51:46.317523" -======= - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-10T12:41:34.562023" ->>>>>>> dev }, "multiqc_stub": { "content": [ @@ -28,7 +17,6 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", -<<<<<<< HEAD "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], @@ -37,21 +25,10 @@ "nextflow": "24.04.4" }, "timestamp": "2024-10-02T17:52:20.680978" -======= - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-10T11:27:11.933869532" ->>>>>>> dev }, "multiqc_versions_config": { "content": [ [ -<<<<<<< HEAD "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], @@ -60,15 +37,5 @@ "nextflow": "24.04.4" }, "timestamp": "2024-10-02T17:52:09.185842" -======= - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-10T11:26:56.709849369" ->>>>>>> dev } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a6..4d7f09c04 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 8b1156767..805dcc424 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -350,12 +350,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def colors = logColours(monochrome_logs) as Map if (email_address) { try { -<<<<<<< HEAD if (plaintext_email) { new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } -======= - if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } ->>>>>>> dev // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -373,21 +369,13 @@ new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } -<<<<<<< HEAD nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") -======= - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); ->>>>>>> dev output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } -<<<<<<< HEAD nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") -======= - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); ->>>>>>> dev output_tf.delete() } @@ -414,18 +402,12 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] -<<<<<<< HEAD summary_params .keySet() .sort() .each { group -> summary << summary_params[group] } -======= - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } ->>>>>>> dev def misc_fields = [:] misc_fields['start'] = workflow.start diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index e58d744b4..b825a5ce0 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -49,8 +49,8 @@ include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV } from '../../mod // // SUBWORKFLOW: Consisting entirely of nf-core/modules // -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { fromList } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { FASTQ_ALIGN_HISAT2 } from '../../subworkflows/nf-core/fastq_align_hisat2' @@ -111,7 +111,7 @@ workflow RNASEQ { // Create channel from input file provided through params.input // Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { From ee83375f480ca8afca7c3a121d4b9d2d47ce06f8 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 9 Oct 2024 15:58:22 +0200 Subject: [PATCH 04/35] Apply suggestions from code review --- CITATIONS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 00a646653..5eaeea7f8 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -26,7 +26,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/) @@ -48,7 +48,7 @@ - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) -> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. - [picard-tools](http://broadinstitute.github.io/picard) From 35b36db3b986f819cf17817d9eaf179230fa86c5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:03:13 +0200 Subject: [PATCH 05/35] fix nf-core lint --- nextflow.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index e70c06529..c2c682e86 100644 --- a/nextflow.config +++ b/nextflow.config @@ -356,10 +356,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """ } summary { From b47c5262a7f695116aeeed0954a03871aa02fdc6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:13:27 +0200 Subject: [PATCH 06/35] install nf-test 0.9.0 --- .github/workflows/ci.yml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e41dc7542..f3a4c690f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,11 +7,11 @@ on: workflow_dispatch: env: - NXF_ANSI_LOG: false + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" NFT_VER: "0.9.0" NFT_WORKDIR: "~" - NFT_DIFF: "pdiff" - NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" + NXF_ANSI_LOG: false concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -63,6 +63,11 @@ jobs: with: version: "${{ matrix.NXF_VER }}" + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} + - uses: actions/setup-python@v4 with: python-version: "3.11" From fc80d92d8aa2bc056bff063586262a5aeaa7f0aa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:16:30 +0200 Subject: [PATCH 07/35] install nf-test once only --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f3a4c690f..ef022099b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -78,8 +78,6 @@ jobs: python -m pip install --upgrade pip pip install pdiff - - uses: nf-core/setup-nf-test@v1 - - name: Run nf-test run: | nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap From a24e284332cb7f5ecef07bdfd7883a7411d144d2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:21:05 +0200 Subject: [PATCH 08/35] use proper Channel factory --- workflows/rnaseq/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index b825a5ce0..2ac6dcf86 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -50,7 +50,7 @@ include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV } from '../../mod // SUBWORKFLOW: Consisting entirely of nf-core/modules // include { paramsSummaryMap } from 'plugin/nf-schema' -include { fromList } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { FASTQ_ALIGN_HISAT2 } from '../../subworkflows/nf-core/fastq_align_hisat2' From 76a1375343fd4d57f41d52183d4fa716e36aa60d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:28:06 +0200 Subject: [PATCH 09/35] rename function test --- ...t => main.pipeline_initialisation.workflow.nf.test} | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) rename subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/{main.pipeline_initialistion.workflow.nf.test => main.pipeline_initialisation.workflow.nf.test} (86%) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test similarity index 86% rename from subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test rename to subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test index c1db3fda8..d7c4f817f 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test @@ -29,12 +29,10 @@ nextflow_workflow { workflow { """ input[0] = false // version (boolean) - input[1] = false // help (boolean) - input[2] = "${projectDir}/nextflow_schema.json" // schema (string) - input[3] = true // validate_parameters (boolean) - input[4] = true // monochrome_logs (boolean) - input[5] = args // args (array) - input[6] = file("$outputDir") // outdir (string) + input[2] = true // validate_parameters (boolean) + input[3] = true // monochrome_logs (boolean) + input[4] = args // args (array) + input[5] = file("$outputDir") // outdir (string) """ } } From 382189c52f1f44a9db2e5452893c4046737a5b70 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:30:58 +0200 Subject: [PATCH 10/35] fix align --- subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index 203d28078..c18c8ce41 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -33,7 +33,7 @@ workflow PIPELINE_INITIALISATION { version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs - nextflow_cli_args // array: List of positional nextflow CLI args + nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved main: From 89444809936d8f14e1acff58352de8ed28741116 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:45:15 +0200 Subject: [PATCH 11/35] fix samplesheet usage --- main.nf | 1 - nextflow_schema.json | 8 -------- .../local/utils_nfcore_rnaseq_pipeline/main.nf | 10 ++++------ 3 files changed, 4 insertions(+), 15 deletions(-) diff --git a/main.nf b/main.nf index f4d539b46..74599c9f0 100755 --- a/main.nf +++ b/main.nf @@ -159,7 +159,6 @@ workflow { // SUBWORKFLOW: Run completion tasks // PIPELINE_COMPLETION ( - "nextflow_schema.json", params.email, params.email_on_fail, params.plaintext_email, diff --git a/nextflow_schema.json b/nextflow_schema.json index e2dd3d2e0..802209b42 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -196,14 +196,6 @@ "fa_icon": "fas fa-indent", "help_text": "The feature type used from the GTF file when generating the biotype plot with featureCounts." }, - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes/", - "fa_icon": "fas fa-cloud-download-alt", - "hidden": true - }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index c18c8ce41..c384222be 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -38,6 +38,8 @@ workflow PIPELINE_INITIALISATION { main: + ch_versions = Channel.empty() + // // Print version and exit if required and dump pipeline parameters to JSON file // @@ -86,14 +88,10 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { samplesheet -> - validateInputSamplesheet(samplesheet) - } .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] + checkSamplesAfterGrouping(it) } - .set { ch_samplesheet } + .set{ ch_samplesheet } emit: samplesheet = ch_samplesheet From c71d10397770d3afdb0d182e194ba8ddd4da6599 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 16:48:21 +0200 Subject: [PATCH 12/35] fix tests --- .../main.pipeline_initialisation.workflow.nf.test | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test index d7c4f817f..87e498887 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test @@ -28,11 +28,11 @@ nextflow_workflow { } workflow { """ - input[0] = false // version (boolean) - input[2] = true // validate_parameters (boolean) - input[3] = true // monochrome_logs (boolean) - input[4] = args // args (array) - input[5] = file("$outputDir") // outdir (string) + input[0] = false // version (boolean) + input[1] = true // validate_parameters (boolean) + input[2] = true // monochrome_logs (boolean) + input[3] = args // args (array) + input[4] = file("$outputDir") // outdir (string) """ } } From 35a94de4f206fdbb41ffed58e258f697deec0dad Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 17:57:39 +0200 Subject: [PATCH 13/35] fix tests --- .../main.pipeline_completion.workflow.nf.test | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test index ea784ea01..3c1440f1a 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test @@ -9,17 +9,16 @@ nextflow_workflow { when { workflow { """ - input[0] = "${projectDir}/nextflow_schema.json" // schema (string) - input[1] = null // email (string) - input[2] = null // email_on_fail (string) - input[3] = true // plaintext_email (boolean) - input[4] = "${outputDir}" // outputDir (string) - input[5] = true // monochrome_logs (boolean) - input[6] = null // hook_url (string) - input[7] = "${outputDir}/multiqc_report.html" // multiqc_report (string) + input[0] = null // email (string) + input[1] = null // email_on_fail (string) + input[2] = true // plaintext_email (boolean) + input[3] = "${outputDir}" // outputDir (string) + input[4] = true // monochrome_logs (boolean) + input[5] = null // hook_url (string) + input[6] = "${outputDir}/multiqc_report.html" // multiqc_report (string) + input[7] = Channel.of(['test_sample', true]) input[8] = Channel.of(['test_sample', true]) input[9] = Channel.of(['test_sample', true]) - input[10] = Channel.of(['test_sample', true]) """ } } From 76c56167a2fe39af63b77fa08694febae7c108fc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 17:57:49 +0200 Subject: [PATCH 14/35] update CHANGELOG --- CHANGELOG.md | 35 +++++++++++++++++++++++++++++++++-- 1 file changed, 33 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 669cd30f2..7d45d8e28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,14 +7,45 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Credits +Special thanks to the following for their contributions to the release: + +- [Maxime Garcia](https://github.com/maxulysse) +- [Jonathan Manning](https://github.com/pinin4fjords) + ### Enhancements & fixes - [PR #1398](https://github.com/nf-core/rnaseq/pull/1398) - Bump pipeline version to 3.17.0dev +- [PR #1401](https://github.com/nf-core/rnaseq/pull/1401) - Template update for nf-core/tools v3.0.1 ### Parameters +| Old parameter | New parameter | +| ------------------------------------ | --------------- | +| | `--help_full` | +| | `--show_hidden` | +| `--validationFailUnrecognisedParams` | | +| `--validationLenientMode` | | +| `--validationSchemaIgnoreParams` | | +| `--validationShowHiddenParams` | | + +> **NB:** Parameter has been **updated** if both old and new parameter information is present. +> +> **NB:** Parameter has been **added** if just the new parameter information is present. +> +> **NB:** Parameter has been **removed** if new parameter information isn't present. + ### Software dependencies +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `MultiQC` | 1.24.1 | 1.25.1 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. + ## [[3.16.0](https://github.com/nf-core/rnaseq/releases/tag/3.16.0)] - 2024-10-02 ### Credits @@ -58,8 +89,8 @@ Special thanks to the following for their contributions to the release: | Dependency | Old version | New version | | ---------- | ----------- | ----------- | -| `Kraken2` | ----------- | 2.1.3 | -| `Bracken` | ----------- | 2.9 | +| `Kraken2` | | 2.1.3 | +| `Bracken` | | 2.9 | > **NB:** Dependency has been **updated** if both old and new version information is present. > From 452850a8790c534bd472e89a521faae2cbaeaebc Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 9 Oct 2024 18:23:41 +0200 Subject: [PATCH 15/35] Apply suggestions from code review --- subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index c384222be..2aa411a68 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -628,8 +628,8 @@ def getInferexperimentStrandedness(inferexperiment_file, stranded_threshold = 0. if (pe_antisense_matcher) reverseFragments = pe_antisense_matcher[0][1].toFloat() * 100 } - return calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragments, stranded_threshold, unstranded_threshold) // Use shared calculation function to determine strandedness + return calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragments, stranded_threshold, unstranded_threshold) } // From 99eeff0bace7a3b2d15df807873f10d3ff7173f7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 18:33:41 +0200 Subject: [PATCH 16/35] update test adjacent files --- nf-test.config | 2 +- tests/nextflow.config | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/nf-test.config b/nf-test.config index c843dabec..107881c35 100644 --- a/nf-test.config +++ b/nf-test.config @@ -12,7 +12,7 @@ config { // load the necessary plugins plugins { - load "nft-bam@0.3.0" + load "nft-bam@0.4.0" load "nft-utils@0.0.2" } } diff --git a/tests/nextflow.config b/tests/nextflow.config index 6bf8f2929..86b7ac5b4 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -14,8 +14,6 @@ params { // for hisat2 hisat2_build_memory = '3.GB' - validationSchemaIgnoreParams = 'genomes,igenomes_base,modules_testdata_base_path,pipelines_testdata_base_path' - // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows outdir = 'results' } @@ -31,7 +29,7 @@ process { // Impose same minimum Nextflow version as the pipeline for testing manifest { - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=24.04.2' } // Disable all Nextflow reporting options From 6ed601453c7b60c6785e9dafb60596fd00cf8c8b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 19:20:34 +0200 Subject: [PATCH 17/35] clean nftignore for kallisto --- tests/.nftignore | 137 +++++------------------------------------------ 1 file changed, 14 insertions(+), 123 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index dcbd8d8a8..8382a4ec4 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,125 +1,16 @@ -**/*DupRate_plot.{pdf,r} -**/*Log.out -**/*Log.{final,progress}.out -**/*_fastqc.{html,zip} -**/*_raw.{html,zip} -**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg} -**/*bam_stat.txt -**/*coverage.gtf -**/*fastq.gz_trimming_report.txt -**/*featureCounts.txt.summary -**/*gene.abundance.txt -**/*hisat2.summary -**/*inner_distance* -**/*junction* -**/*markdup.sorted.MarkDuplicates.metrics.txt -**/*markdup.sorted.{bam,bam.bai} -**/*read_distribution.txt -**/*sorted.bam.{flagstat,idxstats,stats} -**/*sortmerna.log -**/*splice_{events,junction}.{pdf,png,svg} -**/*transcripts.gtf -**/*{cnt,model,theta} -**/*{css,gif,js} -**/*{forward,reverse}.bigWig -**/*{genes,isoforms}.results -**/*{pos,seq}.DupRate.xls -**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt} -**/Junction*.png -**/Reads*.png -**/abundance.{h5,tsv} -**/cutadapt_filtered_reads_plot-{cnt,pct}.{pdf,svg} -**/cutadapt_trimmed_sequences_*{pdf,svg} -**/deseq2* -**/dupradar-section-plot.{pdf,svg} -**/fail_mapped_samples_table* -**/fail_strand_check_table* -**/fastqc-status-check-*{pdf,svg} -**/fastqc_adapter_content_plot.{pdf,png,svg} -**/fastqc_overrepresented_sequences_plot*{pdf,svg} -**/fastqc_per_base_*_plot*{pdf,png,svg} -**/fastqc_per_sequence_*{pdf,svg} -**/fastqc_sequence_length_distribution_plot.{pdf,png,svg} -**/fastqc_sequence_{counts,duplication_levels}_plot*{pdf,svg} -**/fastqc_top_overrepresented_sequences_table*{pdf,png,svg,txt} -**/featurecounts_biotype_plot-{cnt,pct}.{pdf,svg} -**/fld.gz -**/flenDist.txt -**/general_stats_table.{pdf,png,svg} -**/hisat2_pe_plot.txt -**/hisat2_se_plot*{png,svg} -**/hisat2_{pe,se}_plot-{cnt,pct}.{pdf,png,svg} -**/junction_saturation_known.txt -**/junction_saturation_novel.txt -**/kallisto_alignment*{pdf,png,svg} -**/kallisto_alignment.txt -**/kallisto_quant.log -**/meta_info.json -**/multiqc_data.json -**/multiqc_dupradar-section-plot.txt -**/multiqc_fail_strand_check_table.txt -**/multiqc_general_stats.txt -**/multiqc_hisat2.txt -**/multiqc_kallisto.txt -**/multiqc_picard_dups.txt -**/multiqc_plots -**/multiqc_report.html -**/multiqc_rsem.txt -**/multiqc_rseqc_bam_stat.txt -**/multiqc_rseqc_infer_experiment.txt -**/multiqc_rseqc_junction_annotation.txt -**/multiqc_rseqc_read_distribution.txt -**/multiqc_salmon.txt -**/multiqc_samtools_flagstat.txt -**/multiqc_samtools_stats.txt -**/multiqc_software_versions.txt -**/multiqc_sortmerna.txt -**/multiqc_sources.txt -**/multiqc_star.txt -**/multiqc_{salmon,star_salmon}_deseq2_pca-plot*txt -**/picard_deduplication-{cnt,pct}.{pdf,png,svg} -**/picard_deduplication.txt -**/qualimapReport.html -**/qualimap_gene_coverage_profile_Counts.{pdf,svg} -**/qualimap_gene_coverage_profile_Normalised.{pdf,svg} -**/qualimap_genomic_origin-{cnt,pct}.{pdf,png,svg} -**/qualimap_genomic_origin.txt -**/qualimap_rnaseq_genome_results.txt -**/quant.genes.sf -**/quant.sf -**/rnaseq_qc_results.txt -**/rsem_assignment_plot-{cnt,pct}.{pdf,png,svg} -**/rsem_assignment_plot.txt -**/rsem_multimapping_rates.{pdf,svg,txt} -**/rseqc_bam_stat.{pdf,png,svg,txt} -**/rseqc_infer_experiment_plot.{pdf,svg} -**/rseqc_inner_* -**/rseqc_junction_* -**/rseqc_read_distribution_* -**/rseqc_read_dups.txt -**/rseqc_read_dups_plot.txt -**/rseqc_read_dups_plot.{pdf,svg} -**/run_info.json -**/salmon_plot.{pdf,png,svg,txt} -**/salmon_quant.log -**/samtools-flagstat* -**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.{pdf,svg} -**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-{cnt,pct}.{pdf,svg} -**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.{pdf,svg} -**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-{cnt,pct}.{pdf,svg} -**/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.{pdf,svg} -**/samtools-idxstats-mapped-reads-plot_Raw_Counts-{cnt,pct}.{pdf,svg} -**/samtools-stats-dp.{pdf,png,svg,txt} -**/sortmerna-detailed-plot-{cnt,pct}.{pdf,svg} -**/sortmerna-detailed-plot.txt -**/star_summary_table.{pdf,png,svg,txt} -**/t_data.ctab -**/{kallisto,salmon}.merged* -**/{salmon,star_rsem}_deseq2_{clustering,pca}-plot.{pdf,png,svg} -**/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg} -**/{samtools,star}_alignment_plot* -**/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg} bbsplit/*.stats.txt +fastqc/*/*fastqc.{html,zip} +kallisto/*/abundance.{h5,tsv} +kallisto/*/kallisto_quant.log +kallisto/*/run_info.json +kallisto/kallisto.* +multiqc/multiqc_report.html +multiqc/multiqc_report_data/kallisto_alignment.txt +multiqc/multiqc_report_data/multiqc_data.json +multiqc/multiqc_report_data/multiqc_general_stats.txt +multiqc/multiqc_report_data/multiqc_kallisto.txt +multiqc/multiqc_report_data/multiqc_software_versions.txt +multiqc/multiqc_report_data/multiqc_sources.txt +multiqc/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} pipeline_info/*.{html,json,txt,yml} -**/deseq2_qc/size_factors/*.txt -star_rsem/log/*.log +trimgalore/*fastq.gz_trimming_report.txt From a69f1cb07f9a0f44cab1c1bcfbfc03048b22c5dc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 19:22:36 +0200 Subject: [PATCH 18/35] minor code polish --- tests/kallisto.nf.test | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 0c6816a59..168ead0df 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -16,9 +16,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -27,7 +27,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } From 50d47968c34d66d46e58b23df2d86c087faaaab1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 19:22:57 +0200 Subject: [PATCH 19/35] kallisto: update snapshots --- tests/kallisto.nf.test.snap | 136 +++++++++++++++++------------------- 1 file changed, 64 insertions(+), 72 deletions(-) diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 4bb2324e3..3071a3ebf 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -133,18 +133,19 @@ "multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/multiqc_report_data/kallisto_alignment.txt", + "multiqc/multiqc_report_data/multiqc.log", "multiqc/multiqc_report_data/multiqc_citations.txt", "multiqc/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/multiqc_report_data/multiqc_data.json", @@ -159,18 +160,18 @@ "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_report_plots/pdf/general_stats_table.pdf", "multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf", "multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf", @@ -179,18 +180,18 @@ "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/multiqc_report_plots/png/general_stats_table.png", "multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png", "multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png", @@ -199,18 +200,18 @@ "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report_plots/svg/general_stats_table.svg", "multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg", "multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg", @@ -230,41 +231,31 @@ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_top_overrepresented_sequences_table.txt:md5,ab365cbc66c7a9ec93539494fb401b97", + "multiqc.log:md5,8ad099f7085cbd858f2a8feadd603c71", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", - "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", - "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", - "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", - "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", - "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", - "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754" + "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:46:44.393695" + "timestamp": "2024-10-09T19:19:07.816437" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -333,13 +324,14 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:47:31.044439" + "timestamp": "2024-10-09T18:56:35.320816" } -} +} \ No newline at end of file From 1acae78c0a65824eb769a1bb14504d809a0859ce Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 19:31:29 +0200 Subject: [PATCH 20/35] update plugin version --- nf-test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-test.config b/nf-test.config index 107881c35..9069ed831 100644 --- a/nf-test.config +++ b/nf-test.config @@ -13,6 +13,6 @@ config { // load the necessary plugins plugins { load "nft-bam@0.4.0" - load "nft-utils@0.0.2" + load "nft-utils@0.0.3" } } From 8d776ac732aa46e8428688153fc44fcd4bda7cf3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 20:09:42 +0200 Subject: [PATCH 21/35] update nftignore --- tests/.nftignore | 1 + tests/kallisto.nf.test.snap | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 8382a4ec4..81c36b82d 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -5,6 +5,7 @@ kallisto/*/kallisto_quant.log kallisto/*/run_info.json kallisto/kallisto.* multiqc/multiqc_report.html +multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt multiqc/multiqc_report_data/kallisto_alignment.txt multiqc/multiqc_report_data/multiqc_data.json multiqc/multiqc_report_data/multiqc_general_stats.txt diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 3071a3ebf..5dabe917f 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -244,7 +244,6 @@ "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_trimmed_top_overrepresented_sequences_table.txt:md5,ab365cbc66c7a9ec93539494fb401b97", "multiqc.log:md5,8ad099f7085cbd858f2a8feadd603c71", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", @@ -334,4 +333,4 @@ }, "timestamp": "2024-10-09T18:56:35.320816" } -} \ No newline at end of file +} From a94823ad51cc15f02124ab37200d613a3f2cb0c4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 9 Oct 2024 20:14:07 +0200 Subject: [PATCH 22/35] update fastq_fastqc_umitools_trimgalore --- modules.json | 6 +- .../nf-core/bracken/bracken/tests/tags.yml | 2 - .../nf-core/kraken2/kraken2/tests/tags.yml | 3 - modules/nf-core/trimgalore/meta.yml | 101 +++++++++++------- modules/nf-core/umitools/extract/meta.yml | 64 ++++++----- .../umitools/extract/tests/main.nf.test | 1 - .../tests/main.nf.test.snap | 6 +- 7 files changed, 108 insertions(+), 75 deletions(-) delete mode 100644 modules/nf-core/bracken/bracken/tests/tags.yml delete mode 100644 modules/nf-core/kraken2/kraken2/tests/tags.yml diff --git a/modules.json b/modules.json index 02127acb3..f4460822d 100644 --- a/modules.json +++ b/modules.json @@ -244,7 +244,7 @@ }, "trimgalore": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { @@ -269,7 +269,7 @@ }, "umitools/extract": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "umitools/prepareforrsem": { @@ -332,7 +332,7 @@ }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", - "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", + "git_sha": "53fcc37e256ea30818fb793bbe98b63e4a40deb8", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { diff --git a/modules/nf-core/bracken/bracken/tests/tags.yml b/modules/nf-core/bracken/bracken/tests/tags.yml deleted file mode 100644 index 6a2cbd384..000000000 --- a/modules/nf-core/bracken/bracken/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bracken/bracken: - - "modules/nf-core/bracken/bracken/**" diff --git a/modules/nf-core/kraken2/kraken2/tests/tags.yml b/modules/nf-core/kraken2/kraken2/tests/tags.yml deleted file mode 100644 index 9ebfd7ab6..000000000 --- a/modules/nf-core/kraken2/kraken2/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -kraken2/kraken2: - - modules/nf-core/kraken2/kraken2/** - - modules/nf-core/untar/** diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e649088ce..576cb4c59 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -14,50 +14,77 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: | - List of input adapter trimmed FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. - pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{3prime,5prime,trimmed,val}*.fq.gz": + type: file + description: | + List of input adapter trimmed FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. + pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Trim Galore! trimming report + pattern: "*_{report.txt}" - unpaired: - type: file - description: | - FastQ files containing unpaired reads from read 1 or read 2 - pattern: "*unpaired*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*unpaired*.fq.gz": + type: file + description: | + FastQ files containing unpaired reads from read 1 or read 2 + pattern: "*unpaired*.fq.gz" - html: - type: file - description: FastQC report (optional) - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report (optional) + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive (optional) - pattern: "*_{fastqc.zip}" - - log: - type: file - description: Trim Galore! trimming report - pattern: "*_{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive (optional) + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml index 7695b2717..648ffbd26 100644 --- a/modules/nf-core/umitools/extract/meta.yml +++ b/modules/nf-core/umitools/extract/meta.yml @@ -1,5 +1,6 @@ name: umitools_extract -description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place +description: Extracts UMI barcode from a read and add it to the read name, leaving + any sample barcode in place keywords: - UMI - barcode @@ -8,38 +9,49 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: "MIT" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: list - description: | - List of input FASTQ files whose UMIs will be extracted. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: > - Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: > + Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. + | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" - log: - type: file - description: Logfile for umi_tools - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Logfile for umi_tools + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test index 3eec566be..fc90a7a06 100644 --- a/modules/nf-core/umitools/extract/tests/main.nf.test +++ b/modules/nf-core/umitools/extract/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_EXTRACT" config "./nextflow.config" - test("single end") { when { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index b37a75c9b..264ffb222 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -377,14 +377,14 @@ ], [ - + null ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.09.0" }, - "timestamp": "2024-07-22T17:05:49.455992" + "timestamp": "2024-10-09T19:19:22.192915" }, "test single end read with UMI - stub": { "content": [ From 711e66dd5ac7e3f4b77d3508d0902615544aa5d8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 07:29:43 +0200 Subject: [PATCH 23/35] update nftignore and snapshots for salmon and kallisto --- tests/.nftignore | 10 +++ tests/kallisto.nf.test | 6 +- tests/kallisto.nf.test.snap | 1 - tests/salmon.nf.test | 12 ++-- tests/salmon.nf.test.snap | 134 +++++++++++++++++------------------- 5 files changed, 81 insertions(+), 82 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 81c36b82d..e86a3c71c 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -7,11 +7,21 @@ kallisto/kallisto.* multiqc/multiqc_report.html multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt multiqc/multiqc_report_data/kallisto_alignment.txt +multiqc/multiqc_report_data/multiqc.log multiqc/multiqc_report_data/multiqc_data.json multiqc/multiqc_report_data/multiqc_general_stats.txt multiqc/multiqc_report_data/multiqc_kallisto.txt +multiqc/multiqc_report_data/multiqc_salmon.txt multiqc/multiqc_report_data/multiqc_software_versions.txt multiqc/multiqc_report_data/multiqc_sources.txt +multiqc/multiqc_report_data/salmon_plot.txt multiqc/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} pipeline_info/*.{html,json,txt,yml} +salmon/*/aux_info/fld.gz +salmon/*/aux_info/meta_info.json +salmon/*/libParams/flenDist.txt +salmon/*/logs/salmon_quant.log +salmon/*/quant.genes.sf +salmon/*/quant.sf +salmon/salmon.* trimgalore/*fastq.gz_trimming_report.txt diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 168ead0df..a964757d3 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -50,9 +50,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -61,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 5dabe917f..a5402206e 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -244,7 +244,6 @@ "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "multiqc.log:md5,8ad099f7085cbd858f2a8feadd603c71", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233" diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index c0a386da0..562b09cce 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -16,9 +16,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -27,7 +27,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } @@ -50,9 +50,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -61,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 0adf4ff4d..f09490d98 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -88,17 +88,18 @@ "multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_report_data/multiqc.log", "multiqc/multiqc_report_data/multiqc_citations.txt", "multiqc/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/multiqc_report_data/multiqc_data.json", @@ -114,18 +115,18 @@ "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_report_plots/pdf/general_stats_table.pdf", "multiqc/multiqc_report_plots/pdf/salmon_plot.pdf", "multiqc/multiqc_report_plots/png", @@ -133,18 +134,18 @@ "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/multiqc_report_plots/png/general_stats_table.png", "multiqc/multiqc_report_plots/png/salmon_plot.png", "multiqc/multiqc_report_plots/svg", @@ -152,18 +153,18 @@ "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report_plots/svg/general_stats_table.svg", "multiqc/multiqc_report_plots/svg/salmon_plot.svg", "pipeline_info", @@ -275,34 +276,22 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", - "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", - "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", - "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", - "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", - "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", - "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -338,9 +327,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:10:56.056197" + "timestamp": "2024-10-10T07:25:22.063836" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -406,13 +395,14 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:11:32.236118" + "timestamp": "2024-10-10T07:07:48.845197" } -} +} \ No newline at end of file From 4198a88584b037b0dd58a4b2bfd67a4564f3a149 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 09:51:23 +0200 Subject: [PATCH 24/35] no set -C until we fix modules upstream --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index c2c682e86..0c225476d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -297,7 +297,6 @@ bash set -e # Exit if a tool returns a non-zero status/exit code set -u # Treat unset variables and parameters as an error set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. """ // Disable process selector warnings by default. Use debug profile to enable warnings. From b2ac86fb37a2339ffc3e427adf9063e1379dad4e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 09:51:35 +0200 Subject: [PATCH 25/35] update nftignore --- tests/.nftignore | 89 +++++++++++++++++++++++++++++++++++++----------- 1 file changed, 69 insertions(+), 20 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index e86a3c71c..c465f76fb 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,27 +1,76 @@ bbsplit/*.stats.txt -fastqc/*/*fastqc.{html,zip} +fastqc/*/*.{html,zip} kallisto/*/abundance.{h5,tsv} kallisto/*/kallisto_quant.log kallisto/*/run_info.json kallisto/kallisto.* -multiqc/multiqc_report.html -multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt -multiqc/multiqc_report_data/kallisto_alignment.txt -multiqc/multiqc_report_data/multiqc.log -multiqc/multiqc_report_data/multiqc_data.json -multiqc/multiqc_report_data/multiqc_general_stats.txt -multiqc/multiqc_report_data/multiqc_kallisto.txt -multiqc/multiqc_report_data/multiqc_salmon.txt -multiqc/multiqc_report_data/multiqc_software_versions.txt -multiqc/multiqc_report_data/multiqc_sources.txt -multiqc/multiqc_report_data/salmon_plot.txt -multiqc/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} +multiqc/**/multiqc_report.html +multiqc/**/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt +multiqc/**/multiqc_report_data/junction_saturation_known.txt +multiqc/**/multiqc_report_data/junction_saturation_novel.txt +multiqc/**/multiqc_report_data/kallisto_alignment.txt +multiqc/**/multiqc_report_data/multiqc.log +multiqc/**/multiqc_report_data/multiqc_data.json +multiqc/**/multiqc_report_data/multiqc_dupradar.txt +multiqc/**/multiqc_report_data/multiqc_fail_strand_check_table.txt +multiqc/**/multiqc_report_data/multiqc_general_stats.txt +multiqc/**/multiqc_report_data/multiqc_kallisto.txt +multiqc/**/multiqc_report_data/multiqc_picard_dups.txt +multiqc/**/multiqc_report_data/multiqc_rseqc_bam_stat.txt +multiqc/**/multiqc_report_data/multiqc_rseqc_infer_experiment.txt +multiqc/**/multiqc_report_data/multiqc_rseqc_junction_annotation.txt +multiqc/**/multiqc_report_data/multiqc_rseqc_read_distribution.txt +multiqc/**/multiqc_report_data/multiqc_salmon.txt +multiqc/**/multiqc_report_data/multiqc_sample-relationships*.txt +multiqc/**/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt +multiqc/**/multiqc_report_data/multiqc_software_versions.txt +multiqc/**/multiqc_report_data/multiqc_sources.txt +multiqc/**/multiqc_report_data/multiqc_star.txt +multiqc/**/multiqc_report_data/picard_deduplication.txt +multiqc/**/multiqc_report_data/qualimap_genomic_origin.txt +multiqc/**/multiqc_report_data/qualimap_rnaseq_genome_results.txt +multiqc/**/multiqc_report_data/rseqc_bam_stat.txt +multiqc/**/multiqc_report_data/rseqc_inner_distance*.txt +multiqc/**/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt +multiqc/**/multiqc_report_data/rseqc_read_*.txt +multiqc/**/multiqc_report_data/salmon_plot.txt +multiqc/**/multiqc_report_data/samtools-flagstat-dp_*.txt +multiqc/**/multiqc_report_data/samtools-stats-dp.txt +multiqc/**/multiqc_report_data/samtools_alignment_plot.txt +multiqc/**/multiqc_report_data/star_alignment_plot.txt +multiqc/**/multiqc_report_data/star_summary_table.txt +multiqc/**/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} pipeline_info/*.{html,json,txt,yml} -salmon/*/aux_info/fld.gz -salmon/*/aux_info/meta_info.json -salmon/*/libParams/flenDist.txt -salmon/*/logs/salmon_quant.log -salmon/*/quant.genes.sf -salmon/*/quant.sf -salmon/salmon.* +star_salmon/*.{bam,bam.bai} +star_salmon/bigwig/*.{forward,reverse}.bigWig +star_salmon/dupradar/box_plot/*_duprateExpBoxplot.pdf +star_salmon/dupradar/histogram/*_expressionHist.pdf +star_salmon/dupradar/scatter_plot/*_duprateExpDens.pdf +star_salmon/featurecounts/*.featureCounts.txt.summary +star_salmon/log/*.Log.{final.out,out,progress.out} +star_salmon/picard_metrics/*.MarkDuplicates.metrics.txt +star_salmon/qualimap/*/css/* +star_salmon/qualimap/*/images_qualimapReport/* +star_salmon/qualimap/*/qualimapReport.html +star_salmon/qualimap/*/rnaseq_qc_results.txt +star_salmon/rseqc/bam_stat/*.bam_stat.txt +star_salmon/rseqc/read_distribution/*.read_distribution.txt +star_salmon/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* +star_salmon/samtools_stats/*.bam.{flagstat,idxstats,stats} +star_salmon/stringtie/*.ballgown/t_data.ctab +star_salmon/stringtie/*.gene.abundance.txt +star_salmon/stringtie/*.{coverage,transcripts}.gtf trimgalore/*fastq.gz_trimming_report.txt +{salmon,star_salmon}/*/aux_info/fld.gz +{salmon,star_salmon}/*/aux_info/meta_info.json +{salmon,star_salmon}/*/libParams/flenDist.txt +{salmon,star_salmon}/*/logs/salmon_quant.log +{salmon,star_salmon}/*/quant.genes.sf +{salmon,star_salmon}/*/quant.sf +{salmon,star_salmon}/deseq2_qc/deseq2.dds.RData +{salmon,star_salmon}/deseq2_qc/deseq2.pca.vals.txt +{salmon,star_salmon}/deseq2_qc/deseq2.plots.pdf +{salmon,star_salmon}/deseq2_qc/deseq2.sample.dists.txt +{salmon,star_salmon}/deseq2_qc/size_factors/*.txt +{salmon,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData +{salmon,star_salmon}/salmon.* From 2ce830b881c3a0bbbbde8de30456aa82b28f7529 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 09:51:59 +0200 Subject: [PATCH 26/35] update default tests --- tests/default.nf.test | 18 +- tests/default.nf.test.snap | 416 ++++++++++++++----------------------- 2 files changed, 164 insertions(+), 270 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 80b19646a..998e136d8 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -13,9 +13,11 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -24,9 +26,11 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents - stable_path + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } ).match() } ) } @@ -44,9 +48,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -55,7 +59,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5bddc1cff..7ed40b6cc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -83,14 +83,15 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:30:25.608093" + "timestamp": "2024-10-10T09:21:27.152841" }, "Params: default": { "content": [ @@ -283,34 +284,35 @@ "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", - "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -322,24 +324,16 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", @@ -379,32 +373,32 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -428,9 +422,8 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -444,40 +437,38 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_salmon/multiqc_report_plots/png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", @@ -501,9 +492,8 @@ "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -517,40 +507,38 @@ "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_salmon/multiqc_report_plots/svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", @@ -574,9 +562,8 @@ "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -590,8 +577,6 @@ "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", @@ -1301,33 +1286,34 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1340,39 +1326,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6", - "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", - "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", - "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", - "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", - "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", - "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", - "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", - "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", - "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", - "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", - "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", - "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", - "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", - "featurecounts_biotype_plot-cnt.png:md5,4c66fce934b018143e7b8f6a1383d3f6", - "featurecounts_biotype_plot-pct.png:md5,9191dc2dd130f22ad404d27e045d2304", - "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", - "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", - "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1461,103 +1414,18 @@ "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", 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"6c1e33dc619c8ad4799f7cf39dcf2d2f" + ], + [ + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "bbd70318082b935fce75ee323d5dba50" + ], + [ + "WT_REP1.markdup.sorted.bam", + "255c653935697006430033367caa9669" + ], + [ + "WT_REP2.markdup.sorted.bam", + "fce663681eba11bdd48c67d4281d7d4d" + ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.08.0" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:39:09.000328" + "timestamp": "2024-10-10T09:48:14.477734" } -} +} \ No newline at end of file From e5c8c9dc53839b1ec5182a9d8c79be5a3d9fa6ff Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 10:03:36 +0200 Subject: [PATCH 27/35] update featurecounts_group_type tests --- tests/featurecounts_group_type.nf.test | 18 +- tests/featurecounts_group_type.nf.test.snap | 414 ++++++++------------ 2 files changed, 164 insertions(+), 268 deletions(-) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index fcd11c1da..4b88591d6 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -14,9 +14,11 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +27,11 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents - stable_path + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } ).match() } ) } @@ -46,9 +50,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index d1f6cfb9c..95143abfb 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -83,14 +83,15 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:38:08.811967" + "timestamp": "2024-10-10T10:00:44.36432" }, "Params: --featurecounts_group_type false": { "content": [ @@ -277,34 +278,35 @@ "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", - "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -315,24 +317,16 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", @@ -372,32 +366,32 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf", @@ -419,9 +413,8 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -435,40 +428,38 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_salmon/multiqc_report_plots/png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png", @@ -490,9 +481,8 @@ "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -506,40 +496,38 @@ "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_salmon/multiqc_report_plots/svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg", @@ -561,9 +549,8 @@ "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -577,8 +564,6 @@ "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", @@ -1267,33 +1252,34 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,b4776accd1bf7206c7ab0f1d84e4721e", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1305,37 +1291,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - 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"coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "Coverage Profile Along Genes 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"coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6", - "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5", - "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b", - "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1535,12 +1405,34 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ], + [ + [ + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "76476167553ce185faf6fa44b01d34da" + ], + [ + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "c3384e7240bc0291f4c6e3fb91f6cc82" + ], + [ + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "1db43d2a4ad9d37865e0777bf943deaf" + ], + [ + "WT_REP1.markdup.sorted.bam", + "afa34b079825ffdcc260968053509ef3" + ], + [ + "WT_REP2.markdup.sorted.bam", + "fd478d307f2c27138b0ff003b904c481" + ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:37:24.538529" + "timestamp": "2024-10-10T10:00:00.235948" } -} +} \ No newline at end of file From 20e5e7d8f5bf15cc7c763b026025fa2a90b3f51b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 10:28:45 +0200 Subject: [PATCH 28/35] update nftignore and hisat2 snapshots --- tests/.nftignore | 39 ++-- tests/hisat2.nf.test | 18 +- tests/hisat2.nf.test.snap | 403 ++++++++++++++------------------------ 3 files changed, 183 insertions(+), 277 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index c465f76fb..6c805538d 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -40,27 +40,30 @@ multiqc/**/multiqc_report_data/samtools_alignment_plot.txt multiqc/**/multiqc_report_data/star_alignment_plot.txt multiqc/**/multiqc_report_data/star_summary_table.txt multiqc/**/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} +multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt +multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt +multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt pipeline_info/*.{html,json,txt,yml} -star_salmon/*.{bam,bam.bai} -star_salmon/bigwig/*.{forward,reverse}.bigWig -star_salmon/dupradar/box_plot/*_duprateExpBoxplot.pdf -star_salmon/dupradar/histogram/*_expressionHist.pdf -star_salmon/dupradar/scatter_plot/*_duprateExpDens.pdf -star_salmon/featurecounts/*.featureCounts.txt.summary star_salmon/log/*.Log.{final.out,out,progress.out} -star_salmon/picard_metrics/*.MarkDuplicates.metrics.txt -star_salmon/qualimap/*/css/* -star_salmon/qualimap/*/images_qualimapReport/* -star_salmon/qualimap/*/qualimapReport.html -star_salmon/qualimap/*/rnaseq_qc_results.txt -star_salmon/rseqc/bam_stat/*.bam_stat.txt -star_salmon/rseqc/read_distribution/*.read_distribution.txt -star_salmon/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* -star_salmon/samtools_stats/*.bam.{flagstat,idxstats,stats} -star_salmon/stringtie/*.ballgown/t_data.ctab -star_salmon/stringtie/*.gene.abundance.txt -star_salmon/stringtie/*.{coverage,transcripts}.gtf trimgalore/*fastq.gz_trimming_report.txt +{hisat2,star_salmon}/*.{bam,bam.bai} +{hisat2,star_salmon}/bigwig/*.{forward,reverse}.bigWig +{hisat2,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf +{hisat2,star_salmon}/dupradar/histogram/*_expressionHist.pdf +{hisat2,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf +{hisat2,star_salmon}/featurecounts/*.featureCounts.txt.summary +{hisat2,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt +{hisat2,star_salmon}/qualimap/*/css/* +{hisat2,star_salmon}/qualimap/*/images_qualimapReport/* +{hisat2,star_salmon}/qualimap/*/qualimapReport.html +{hisat2,star_salmon}/qualimap/*/rnaseq_qc_results.txt +{hisat2,star_salmon}/rseqc/bam_stat/*.bam_stat.txt +{hisat2,star_salmon}/rseqc/read_distribution/*.read_distribution.txt +{hisat2,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* +{hisat2,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} +{hisat2,star_salmon}/stringtie/*.ballgown/t_data.ctab +{hisat2,star_salmon}/stringtie/*.gene.abundance.txt +{hisat2,star_salmon}/stringtie/*.{coverage,transcripts}.gtf {salmon,star_salmon}/*/aux_info/fld.gz {salmon,star_salmon}/*/aux_info/meta_info.json {salmon,star_salmon}/*/libParams/flenDist.txt diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index e743a37d4..6f3f6c3fa 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -14,9 +14,11 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +27,11 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents - stable_path + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } ).match() } ) } @@ -46,9 +50,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 8899222be..5d35018ab 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -84,14 +84,15 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:43:50.371605" + "timestamp": "2024-10-10T10:10:47.69497" }, "Params: --aligner hisat2": { "content": [ @@ -750,36 +751,37 @@ "multiqc/hisat2/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt", "multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt", "multiqc/hisat2/multiqc_report_data/junction_saturation_known.txt", "multiqc/hisat2/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/hisat2/multiqc_report_data/multiqc.log", "multiqc/hisat2/multiqc_report_data/multiqc_citations.txt", "multiqc/hisat2/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/hisat2/multiqc_report_data/multiqc_data.json", - "multiqc/hisat2/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/hisat2/multiqc_report_data/multiqc_dupradar.txt", "multiqc/hisat2/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -792,12 +794,8 @@ "multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt", - "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/hisat2/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/hisat2/multiqc_report_data/multiqc_sample-relationships_1.txt", "multiqc/hisat2/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt", @@ -840,32 +838,32 @@ "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -893,9 +891,8 @@ "multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/hisat2/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -912,32 +909,32 @@ "multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - 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"multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1368,39 +1278,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", - 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"fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", - "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", - "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", - "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46", - "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338", - "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", - "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", - "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", - "rseqc_read_dups_plot.png:md5,fbb8a2268f0468be5a94c960bd2ebd2a", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,a56226e705754ce81c7709d40794dd92", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1433,12 +1310,34 @@ "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ], + [ + [ + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "4bf1f3b76f3530504adfdb43b2108d8b" + ], + [ + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "2296ff6525d6efb9ffa5b3dcc870dd0d" + ], + [ + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "799583958cd2ca6ad49be00651a33359" + ], + [ + "WT_REP1.markdup.sorted.bam", + "aea452c12ed0a10dee2f1b004a7dad95" + ], + [ + "WT_REP2.markdup.sorted.bam", + "6c30c16afec17c44cddfcc9eacea5cd2" + ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:43:07.13584" + "timestamp": "2024-10-10T10:25:14.209047" } -} +} \ No newline at end of file From 997fb251622e6d3e097e8ea066ba2f23dbcda8ea Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 10:42:11 +0200 Subject: [PATCH 29/35] update min_mapped_reads snapshots --- tests/.nftignore | 72 +++--- tests/min_mapped_reads.nf.test | 18 +- tests/min_mapped_reads.nf.test.snap | 374 +++++++++++----------------- 3 files changed, 192 insertions(+), 272 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 6c805538d..ce7674277 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -4,42 +4,42 @@ kallisto/*/abundance.{h5,tsv} kallisto/*/kallisto_quant.log kallisto/*/run_info.json kallisto/kallisto.* -multiqc/**/multiqc_report.html -multiqc/**/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt -multiqc/**/multiqc_report_data/junction_saturation_known.txt -multiqc/**/multiqc_report_data/junction_saturation_novel.txt -multiqc/**/multiqc_report_data/kallisto_alignment.txt -multiqc/**/multiqc_report_data/multiqc.log -multiqc/**/multiqc_report_data/multiqc_data.json -multiqc/**/multiqc_report_data/multiqc_dupradar.txt -multiqc/**/multiqc_report_data/multiqc_fail_strand_check_table.txt -multiqc/**/multiqc_report_data/multiqc_general_stats.txt -multiqc/**/multiqc_report_data/multiqc_kallisto.txt -multiqc/**/multiqc_report_data/multiqc_picard_dups.txt -multiqc/**/multiqc_report_data/multiqc_rseqc_bam_stat.txt -multiqc/**/multiqc_report_data/multiqc_rseqc_infer_experiment.txt -multiqc/**/multiqc_report_data/multiqc_rseqc_junction_annotation.txt -multiqc/**/multiqc_report_data/multiqc_rseqc_read_distribution.txt -multiqc/**/multiqc_report_data/multiqc_salmon.txt -multiqc/**/multiqc_report_data/multiqc_sample-relationships*.txt -multiqc/**/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt -multiqc/**/multiqc_report_data/multiqc_software_versions.txt -multiqc/**/multiqc_report_data/multiqc_sources.txt -multiqc/**/multiqc_report_data/multiqc_star.txt -multiqc/**/multiqc_report_data/picard_deduplication.txt -multiqc/**/multiqc_report_data/qualimap_genomic_origin.txt -multiqc/**/multiqc_report_data/qualimap_rnaseq_genome_results.txt -multiqc/**/multiqc_report_data/rseqc_bam_stat.txt -multiqc/**/multiqc_report_data/rseqc_inner_distance*.txt -multiqc/**/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt -multiqc/**/multiqc_report_data/rseqc_read_*.txt -multiqc/**/multiqc_report_data/salmon_plot.txt -multiqc/**/multiqc_report_data/samtools-flagstat-dp_*.txt -multiqc/**/multiqc_report_data/samtools-stats-dp.txt -multiqc/**/multiqc_report_data/samtools_alignment_plot.txt -multiqc/**/multiqc_report_data/star_alignment_plot.txt -multiqc/**/multiqc_report_data/star_summary_table.txt -multiqc/**/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} +{multiqc,multiqc/**}/multiqc_report.html +{multiqc,multiqc/**}/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt +{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt +{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt +{multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc.log +{multiqc,multiqc/**}/multiqc_report_data/multiqc_data.json +{multiqc,multiqc/**}/multiqc_report_data/multiqc_dupradar.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_fail_strand_check_table.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_bam_stat.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_read_distribution.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_sample-relationships*.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_software_versions.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_sources.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_star.txt +{multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt +{multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt +{multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt +{multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt +{multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt +{multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt +{multiqc,multiqc/**}/multiqc_report_data/rseqc_read_*.txt +{multiqc,multiqc/**}/multiqc_report_data/salmon_plot.txt +{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-dp_*.txt +{multiqc,multiqc/**}/multiqc_report_data/samtools-stats-dp.txt +{multiqc,multiqc/**}/multiqc_report_data/samtools_alignment_plot.txt +{multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt +{multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt +{multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 7ffef71de..eb4224f19 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -14,9 +14,11 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +27,11 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents - stable_path + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } ).match() } ) } @@ -46,9 +50,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index ce656d979..93942231f 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -190,34 +190,35 @@ "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", - "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_mapped_samples_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", @@ -230,24 +231,16 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", @@ -287,33 +280,33 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -337,9 +330,8 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -353,41 +345,39 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_salmon/multiqc_report_plots/png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", @@ -411,9 +401,8 @@ "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -427,41 +416,39 @@ "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_salmon/multiqc_report_plots/svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_mapped_samples_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", @@ -485,9 +472,8 @@ "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -501,8 +487,6 @@ "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", @@ -1042,34 +1026,35 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1082,39 +1067,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582", - "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", - "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", - "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", - "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", - "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", - "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", - "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", - "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", - "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", - "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", - "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", - "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", - "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", - "featurecounts_biotype_plot-cnt.png:md5,95b10627fff1af0a209b8e380f4a4d0b", - "featurecounts_biotype_plot-pct.png:md5,f9c1cf03824ff9ba7da8537ecd93945b", - "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c", - "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e", - "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42", - "rseqc_read_dups_plot.png:md5,bdc7281c52b54a5784aa0d714f9c255e", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1193,63 +1145,12 @@ "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", - "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", - "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", - "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", - "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", - "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", - "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", - "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", - "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", - "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", @@ -1269,13 +1170,27 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ], + [ + [ + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "542a64613e641be18a172830f281b319" + ], + [ + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "42765cd169f11cb21c4ca680b1f8f200" + ], + [ + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "3146dc95e97f6b3036b046613bb5102f" + ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:54:27.006271" + "timestamp": "2024-10-10T10:36:48.24104" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1361,13 +1276,14 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:55:19.233936" + "timestamp": "2024-10-10T10:37:37.274627" } -} +} \ No newline at end of file From 6866c24af72c7747846846124e961393bd8af757 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 10:56:40 +0200 Subject: [PATCH 30/35] do not snapshot the bam --- tests/.nftignore | 2 +- tests/default.nf.test | 6 +---- tests/default.nf.test.snap | 25 +-------------------- tests/featurecounts_group_type.nf.test | 6 +---- tests/featurecounts_group_type.nf.test.snap | 25 +-------------------- tests/hisat2.nf.test | 6 +---- tests/hisat2.nf.test.snap | 3 +-- tests/min_mapped_reads.nf.test | 6 +---- tests/min_mapped_reads.nf.test.snap | 17 +------------- 9 files changed, 9 insertions(+), 87 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index ce7674277..539f20591 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -5,7 +5,7 @@ kallisto/*/kallisto_quant.log kallisto/*/run_info.json kallisto/kallisto.* {multiqc,multiqc/**}/multiqc_report.html -{multiqc,multiqc/**}/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt +{multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt {multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt diff --git a/tests/default.nf.test b/tests/default.nf.test index 998e136d8..f47aec312 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -16,8 +16,6 @@ nextflow_pipeline { def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - // bam_files: All bam files - def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -28,9 +26,7 @@ nextflow_pipeline { // All stable path name, with a relative path stable_name, // All files with stable contents - stable_path, - // All bam files - bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + stable_path ).match() } ) } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 7ed40b6cc..54f69a54b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1299,7 +1299,6 @@ "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", @@ -1455,28 +1454,6 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" - ], - [ - [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "289857e4f0b6c753038917027f5d88bd" - ], - [ - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "6c1e33dc619c8ad4799f7cf39dcf2d2f" - ], - [ - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "bbd70318082b935fce75ee323d5dba50" - ], - [ - "WT_REP1.markdup.sorted.bam", - "255c653935697006430033367caa9669" - ], - [ - "WT_REP2.markdup.sorted.bam", - "fce663681eba11bdd48c67d4281d7d4d" - ] ] ], "meta": { @@ -1485,4 +1462,4 @@ }, "timestamp": "2024-10-10T09:48:14.477734" } -} \ No newline at end of file +} diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 4b88591d6..daefc3fb6 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -17,8 +17,6 @@ nextflow_pipeline { def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - // bam_files: All bam files - def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -29,9 +27,7 @@ nextflow_pipeline { // All stable path name, with a relative path stable_name, // All files with stable contents - stable_path, - // All bam files - bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + stable_path ).match() } ) } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 95143abfb..5f427d903 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1265,7 +1265,6 @@ "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", @@ -1405,28 +1404,6 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" - ], - [ - [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "76476167553ce185faf6fa44b01d34da" - ], - [ - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "c3384e7240bc0291f4c6e3fb91f6cc82" - ], - [ - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "1db43d2a4ad9d37865e0777bf943deaf" - ], - [ - "WT_REP1.markdup.sorted.bam", - "afa34b079825ffdcc260968053509ef3" - ], - [ - "WT_REP2.markdup.sorted.bam", - "fd478d307f2c27138b0ff003b904c481" - ] ] ], "meta": { @@ -1435,4 +1412,4 @@ }, "timestamp": "2024-10-10T10:00:00.235948" } -} \ No newline at end of file +} diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 6f3f6c3fa..478205889 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -17,8 +17,6 @@ nextflow_pipeline { def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - // bam_files: All bam files - def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -29,9 +27,7 @@ nextflow_pipeline { // All stable path name, with a relative path stable_name, // All files with stable contents - stable_path, - // All bam files - bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + stable_path ).match() } ) } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 5d35018ab..cd54ec4a0 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -761,7 +761,6 @@ "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", - "multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", @@ -1340,4 +1339,4 @@ }, "timestamp": "2024-10-10T10:25:14.209047" } -} \ No newline at end of file +} diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index eb4224f19..0572a71ac 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -17,8 +17,6 @@ nextflow_pipeline { def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - // bam_files: All bam files - def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -29,9 +27,7 @@ nextflow_pipeline { // All stable path name, with a relative path stable_name, // All files with stable contents - stable_path, - // All bam files - bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + stable_path ).match() } ) } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 93942231f..2e0636eb8 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1039,7 +1039,6 @@ "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", @@ -1170,20 +1169,6 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" - ], - [ - [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "542a64613e641be18a172830f281b319" - ], - [ - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "42765cd169f11cb21c4ca680b1f8f200" - ], - [ - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "3146dc95e97f6b3036b046613bb5102f" - ] ] ], "meta": { @@ -1286,4 +1271,4 @@ }, "timestamp": "2024-10-10T10:37:37.274627" } -} \ No newline at end of file +} From 0e2fe1a270c249dcd57bf2d84e915e712510fee9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 11:09:41 +0200 Subject: [PATCH 31/35] update remove_ribo_rna tests --- tests/.nftignore | 51 ++-- tests/remove_ribo_rna.nf.test | 12 +- tests/remove_ribo_rna.nf.test.snap | 393 ++++++++++------------------- 3 files changed, 162 insertions(+), 294 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 539f20591..b8f4c7d25 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -4,6 +4,31 @@ kallisto/*/abundance.{h5,tsv} kallisto/*/kallisto_quant.log kallisto/*/run_info.json kallisto/kallisto.* +multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt +multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt +multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt +pipeline_info/*.{html,json,txt,yml} +sortmerna/*.sortmerna.log +star_salmon/log/*.Log.{final.out,out,progress.out} +trimgalore/*fastq.gz_trimming_report.txt +{hisat2,star_salmon}/*.{bam,bam.bai} +{hisat2,star_salmon}/bigwig/*.{forward,reverse}.bigWig +{hisat2,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf +{hisat2,star_salmon}/dupradar/histogram/*_expressionHist.pdf +{hisat2,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf +{hisat2,star_salmon}/featurecounts/*.featureCounts.txt.summary +{hisat2,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt +{hisat2,star_salmon}/qualimap/*/css/* +{hisat2,star_salmon}/qualimap/*/images_qualimapReport/* +{hisat2,star_salmon}/qualimap/*/qualimapReport.html +{hisat2,star_salmon}/qualimap/*/rnaseq_qc_results.txt +{hisat2,star_salmon}/rseqc/bam_stat/*.bam_stat.txt +{hisat2,star_salmon}/rseqc/read_distribution/*.read_distribution.txt +{hisat2,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* +{hisat2,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} +{hisat2,star_salmon}/stringtie/*.ballgown/t_data.ctab +{hisat2,star_salmon}/stringtie/*.gene.abundance.txt +{hisat2,star_salmon}/stringtie/*.{coverage,transcripts}.gtf {multiqc,multiqc/**}/multiqc_report.html {multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt @@ -24,6 +49,7 @@ kallisto/kallisto.* {multiqc,multiqc/**}/multiqc_report_data/multiqc_sample-relationships*.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_software_versions.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_sortmerna.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_sources.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_star.txt {multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt @@ -37,33 +63,10 @@ kallisto/kallisto.* {multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-dp_*.txt {multiqc,multiqc/**}/multiqc_report_data/samtools-stats-dp.txt {multiqc,multiqc/**}/multiqc_report_data/samtools_alignment_plot.txt +{multiqc,multiqc/**}/multiqc_report_data/sortmerna-detailed-plot.txt {multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt {multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt {multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} -multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt -multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt -multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt -pipeline_info/*.{html,json,txt,yml} -star_salmon/log/*.Log.{final.out,out,progress.out} -trimgalore/*fastq.gz_trimming_report.txt -{hisat2,star_salmon}/*.{bam,bam.bai} -{hisat2,star_salmon}/bigwig/*.{forward,reverse}.bigWig -{hisat2,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf -{hisat2,star_salmon}/dupradar/histogram/*_expressionHist.pdf -{hisat2,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf -{hisat2,star_salmon}/featurecounts/*.featureCounts.txt.summary -{hisat2,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt -{hisat2,star_salmon}/qualimap/*/css/* -{hisat2,star_salmon}/qualimap/*/images_qualimapReport/* -{hisat2,star_salmon}/qualimap/*/qualimapReport.html -{hisat2,star_salmon}/qualimap/*/rnaseq_qc_results.txt -{hisat2,star_salmon}/rseqc/bam_stat/*.bam_stat.txt -{hisat2,star_salmon}/rseqc/read_distribution/*.read_distribution.txt -{hisat2,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* -{hisat2,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} -{hisat2,star_salmon}/stringtie/*.ballgown/t_data.ctab -{hisat2,star_salmon}/stringtie/*.gene.abundance.txt -{hisat2,star_salmon}/stringtie/*.{coverage,transcripts}.gtf {salmon,star_salmon}/*/aux_info/fld.gz {salmon,star_salmon}/*/aux_info/meta_info.json {salmon,star_salmon}/*/libParams/flenDist.txt diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 66084a8c9..361c80372 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -14,9 +14,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } @@ -46,9 +46,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index da224c5e5..232ea90a6 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -196,34 +196,35 @@ "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", - "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -235,12 +236,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", @@ -248,12 +247,6 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", @@ -294,32 +287,32 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -343,9 +336,8 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -361,40 +353,38 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/sortmerna-detailed-plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_salmon/multiqc_report_plots/png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", @@ -418,9 +408,8 @@ "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -436,40 +425,38 @@ "multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_salmon/multiqc_report_plots/svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", @@ -493,9 +480,8 @@ "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -511,8 +497,6 @@ "multiqc/star_salmon/multiqc_report_plots/svg/sortmerna-detailed-plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", @@ -1228,33 +1212,33 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - 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"2024-10-10T11:03:32.596507" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1611,13 +1475,14 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:08:00.752563" + "timestamp": "2024-10-10T11:04:25.816703" } } From 60f73b9ca728b3c3d39100b8d2a06c45d5145891 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 11:20:00 +0200 Subject: [PATCH 32/35] update skip_qc tests --- tests/skip_qc.nf.test | 12 ++-- tests/skip_qc.nf.test.snap | 140 ++++++++++++++++--------------------- 2 files changed, 68 insertions(+), 84 deletions(-) diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 3c03631cc..7861f9962 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -14,9 +14,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } @@ -46,9 +46,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 3d2688737..b85335408 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -69,14 +69,15 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:17:45.954114" + "timestamp": "2024-10-10T11:17:30.991115" }, "Params: --skip_qc": { "content": [ @@ -208,17 +209,18 @@ "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", @@ -252,18 +254,18 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf", @@ -287,18 +289,18 @@ "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png", @@ -322,18 +324,18 @@ "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg", @@ -675,22 +677,22 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -698,24 +700,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", - "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", - "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", - "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", - "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", - "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", - "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -802,8 +786,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:17:03.577873" + "timestamp": "2024-10-10T11:16:41.081492" } -} +} \ No newline at end of file From 76297959831c03ac599bf43253777dc81a059a25 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 11:31:51 +0200 Subject: [PATCH 33/35] update skip_trimming snapshots --- tests/hisat2.nf.test.snap | 22 --- tests/skip_trimming.nf.test | 6 +- tests/skip_trimming.nf.test.snap | 266 +++++++++---------------------- 3 files changed, 75 insertions(+), 219 deletions(-) diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index cd54ec4a0..9de57ae81 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1309,28 +1309,6 @@ "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" - ], - [ - [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "4bf1f3b76f3530504adfdb43b2108d8b" - ], - [ - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "2296ff6525d6efb9ffa5b3dcc870dd0d" - ], - [ - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "799583958cd2ca6ad49be00651a33359" - ], - [ - "WT_REP1.markdup.sorted.bam", - "aea452c12ed0a10dee2f1b004a7dad95" - ], - [ - "WT_REP2.markdup.sorted.bam", - "6c30c16afec17c44cddfcc9eacea5cd2" - ] ] ], "meta": { diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 5053e103f..bb4282216 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -14,9 +14,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 715c0604b..82acf3cfd 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -166,22 +166,23 @@ "multiqc/star_salmon", "multiqc/star_salmon/multiqc_report.html", "multiqc/star_salmon/multiqc_report_data", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", - "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt", @@ -192,24 +193,16 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", @@ -245,20 +238,20 @@ "multiqc/star_salmon/multiqc_report_data/star_summary_table.txt", "multiqc/star_salmon/multiqc_report_plots", "multiqc/star_salmon/multiqc_report_plots/pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -282,9 +275,8 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -298,24 +290,22 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_salmon/multiqc_report_plots/png", - "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", @@ -339,9 +329,8 @@ "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -355,24 +344,22 @@ "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_salmon/multiqc_report_plots/svg", - "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", @@ -396,9 +383,8 @@ "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -412,8 +398,6 @@ "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", @@ -1114,16 +1098,16 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", 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"coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24", "coverage_profile_along_genes_(low).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", @@ -1377,8 +1255,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:24:30.328195" + "timestamp": "2024-10-10T11:28:37.351353" } -} +} \ No newline at end of file From a93e9bbe7f2f42d8bebf7b170323fbbc3dddbc4d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 12:49:45 +0200 Subject: [PATCH 34/35] update last snapshots --- tests/.nftignore | 54 ++--- tests/hisat2.nf.test.snap | 11 +- tests/star_rsem.nf.test | 12 +- tests/star_rsem.nf.test.snap | 396 ++++++++++++----------------------- 4 files changed, 170 insertions(+), 303 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index b8f4c7d25..607d912d5 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,5 +1,6 @@ bbsplit/*.stats.txt fastqc/*/*.{html,zip} +hisat2/log/*.hisat2.summary.log kallisto/*/abundance.{h5,tsv} kallisto/*/kallisto_quant.log kallisto/*/run_info.json @@ -9,26 +10,29 @@ multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt pipeline_info/*.{html,json,txt,yml} sortmerna/*.sortmerna.log +star_rsem/*.stat/*.{cnt,model,theta} +star_rsem/*.{genes,isoforms}.results +star_rsem/log/*.log star_salmon/log/*.Log.{final.out,out,progress.out} trimgalore/*fastq.gz_trimming_report.txt -{hisat2,star_salmon}/*.{bam,bam.bai} -{hisat2,star_salmon}/bigwig/*.{forward,reverse}.bigWig -{hisat2,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf -{hisat2,star_salmon}/dupradar/histogram/*_expressionHist.pdf -{hisat2,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf -{hisat2,star_salmon}/featurecounts/*.featureCounts.txt.summary -{hisat2,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt -{hisat2,star_salmon}/qualimap/*/css/* -{hisat2,star_salmon}/qualimap/*/images_qualimapReport/* -{hisat2,star_salmon}/qualimap/*/qualimapReport.html -{hisat2,star_salmon}/qualimap/*/rnaseq_qc_results.txt -{hisat2,star_salmon}/rseqc/bam_stat/*.bam_stat.txt -{hisat2,star_salmon}/rseqc/read_distribution/*.read_distribution.txt -{hisat2,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* -{hisat2,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} -{hisat2,star_salmon}/stringtie/*.ballgown/t_data.ctab -{hisat2,star_salmon}/stringtie/*.gene.abundance.txt -{hisat2,star_salmon}/stringtie/*.{coverage,transcripts}.gtf +{hisat2,star_rsem,star_salmon}/*.{bam,bam.bai} +{hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig +{hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf +{hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf +{hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf +{hisat2,star_rsem,star_salmon}/featurecounts/*.featureCounts.txt.summary +{hisat2,star_rsem,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt +{hisat2,star_rsem,star_salmon}/qualimap/*/css/* +{hisat2,star_rsem,star_salmon}/qualimap/*/images_qualimapReport/* +{hisat2,star_rsem,star_salmon}/qualimap/*/qualimapReport.html +{hisat2,star_rsem,star_salmon}/qualimap/*/rnaseq_qc_results.txt +{hisat2,star_rsem,star_salmon}/rseqc/bam_stat/*.bam_stat.txt +{hisat2,star_rsem,star_salmon}/rseqc/read_distribution/*.read_distribution.txt +{hisat2,star_rsem,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* +{hisat2,star_rsem,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} +{hisat2,star_rsem,star_salmon}/stringtie/*.ballgown/t_data.ctab +{hisat2,star_rsem,star_salmon}/stringtie/*.gene.abundance.txt +{hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf {multiqc,multiqc/**}/multiqc_report.html {multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt @@ -41,6 +45,7 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_rsem.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_bam_stat.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt @@ -55,6 +60,7 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt {multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt {multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt +{multiqc,multiqc/**}/multiqc_report_data/rsem_assignment_plot.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt @@ -67,16 +73,16 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt {multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt {multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.dds.RData +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.pca.vals.txt +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.plots.pdf +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.sample.dists.txt +{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/*.txt +{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData {salmon,star_salmon}/*/aux_info/fld.gz {salmon,star_salmon}/*/aux_info/meta_info.json {salmon,star_salmon}/*/libParams/flenDist.txt {salmon,star_salmon}/*/logs/salmon_quant.log {salmon,star_salmon}/*/quant.genes.sf {salmon,star_salmon}/*/quant.sf -{salmon,star_salmon}/deseq2_qc/deseq2.dds.RData -{salmon,star_salmon}/deseq2_qc/deseq2.pca.vals.txt -{salmon,star_salmon}/deseq2_qc/deseq2.plots.pdf -{salmon,star_salmon}/deseq2_qc/deseq2.sample.dists.txt -{salmon,star_salmon}/deseq2_qc/size_factors/*.txt -{salmon,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData {salmon,star_salmon}/salmon.* diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 9de57ae81..2fec710ac 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -761,6 +761,7 @@ "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", @@ -1192,11 +1193,6 @@ "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,702446d50a5019c84fcef85d1cfef78c", - "RAP1_IAA_30M_REP1.hisat2.summary.log:md5,4273e7a9d0fa8a93ec62e25a70a7e212", - "RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678", - "RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9", - "WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8", - "WT_REP2.hisat2.summary.log:md5,e622496abff3ce68afcd1c21a7a1e0df", "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536", "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06", "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06", @@ -1250,7 +1246,6 @@ "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_raw_top_overrepresented_sequences_table.txt:md5,b2c138ad689c01aaae91b5850112a964", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", @@ -1315,6 +1310,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.0" }, - "timestamp": "2024-10-10T10:25:14.209047" + "timestamp": "2024-10-10T12:37:31.888584" } -} +} \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 268a1fabb..8c52fb826 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -14,9 +14,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } @@ -46,9 +46,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 51411c86c..1793abee7 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -190,34 +190,35 @@ "multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc.log", "multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_data.json", - "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -230,23 +231,15 @@ "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_1.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_2.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_3.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_4.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt", "multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt", "multiqc/star_rsem/multiqc_report_data/picard_histogram.txt", "multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt", @@ -286,32 +279,32 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -338,9 +331,8 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -352,39 +344,37 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering-plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca-plot.pdf", "multiqc/star_rsem/multiqc_report_plots/png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_rsem/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/dupradar.png", "multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png", @@ -411,9 +401,8 @@ "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -425,39 +414,37 @@ "multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png", - "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca-plot.png", "multiqc/star_rsem/multiqc_report_plots/svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg", @@ -484,9 +471,8 @@ "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -498,8 +484,6 @@ "multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering-plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca-plot.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "salmon", @@ -1139,80 +1123,46 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - 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(Total).png:md5,bb10036285f9e01ed64048597a25766f", - "Transcript coverage histogram.png:md5,e36d2e717f852cc69f2658e6a901a0ec", "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", @@ -1404,9 +1269,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:31:03.022387" + "timestamp": "2024-10-10T12:45:00.993602" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1490,13 +1355,14 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:31:54.433237" + "timestamp": "2024-10-10T11:41:09.240442" } -} +} \ No newline at end of file From 386d6bd9c52d39b63ee90dccf9a21ba5b5771fee Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 13:04:34 +0200 Subject: [PATCH 35/35] ignore file --- tests/.nftignore | 7 ++++--- tests/star_rsem.nf.test.snap | 3 +-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 607d912d5..6d2f0b8a8 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -5,9 +5,6 @@ kallisto/*/abundance.{h5,tsv} kallisto/*/kallisto_quant.log kallisto/*/run_info.json kallisto/kallisto.* -multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt -multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt -multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt pipeline_info/*.{html,json,txt,yml} sortmerna/*.sortmerna.log star_rsem/*.stat/*.{cnt,model,theta} @@ -35,6 +32,8 @@ trimgalore/*fastq.gz_trimming_report.txt {hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf {multiqc,multiqc/**}/multiqc_report.html {multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt +{multiqc,multiqc/**}/multiqc_report_data/hisat2_pe_plot.txt +{multiqc,multiqc/**}/multiqc_report_data/hisat2_se_plot.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt {multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt @@ -43,6 +42,7 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_dupradar.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_fail_strand_check_table.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_hisat2.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rsem.txt @@ -61,6 +61,7 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt {multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt {multiqc,multiqc/**}/multiqc_report_data/rsem_assignment_plot.txt +{multiqc,multiqc/**}/multiqc_report_data/rsem_multimapping_rates.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 1793abee7..cdbf5a543 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1158,7 +1158,6 @@ "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", - "rsem_multimapping_rates.txt:md5,05878dd307fa1666dd4cc1888de6257a", "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", @@ -1365,4 +1364,4 @@ }, "timestamp": "2024-10-10T11:41:09.240442" } -} \ No newline at end of file +}