diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..7fe55006 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +*.config linguist-language=nextflow diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml new file mode 100644 index 00000000..030138a0 --- /dev/null +++ b/.github/.dockstore.yml @@ -0,0 +1,5 @@ +# Dockstore config version, not pipeline version +version: 1.2 +workflows: + - subclass: nfl + primaryDescriptorPath: /nextflow.config diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 00000000..323db0a0 --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,128 @@ +# nf-core/cutandrun: Contributing Guidelines + +Hi there! +Many thanks for taking an interest in improving nf-core/cutandrun. + +We try to manage the required tasks for nf-core/cutandrun using GitHub issues, you probably came to this page when creating one. +Please use the pre-filled template to save time. + +However, don't be put off by this template - other more general issues and suggestions are welcome! +Contributions to the code are even more welcome ;) + +> If you need help using or modifying nf-core/cutandrun then the best place to ask is on the nf-core Slack [#cutandrun](https://nfcore.slack.com/channels/cutandrun) channel ([join our Slack here](https://nf-co.re/join/slack)). + +## Contribution workflow + +If you'd like to write some code for nf-core/cutandrun, the standard workflow is as follows: + +1. Check that there isn't already an issue about your idea in the [nf-core/cutandrun issues](https://github.com/nf-core/cutandrun/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/cutandrun repository](https://github.com/nf-core/cutandrun) 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). +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/). + +## Tests + +When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. +Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. + +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. + +If any failures or warnings are encountered, please follow the listed URL for more documentation. + +### Pipeline tests + +Each `nf-core` pipeline should be set up with a minimal set of test-data. +`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. +If there are any failures then the automated tests fail. +These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. + +## Patch + +:warning: Only in the unlikely and regretful event of a release happening with a bug. + +* On your own fork, make a new branch `patch` based on `upstream/master`. +* Fix the bug, and bump version (X.Y.Z+1). +* A PR should be made on `master` from patch to directly this particular bug. + +## Getting help + +For further information/help, please consult the [nf-core/cutandrun documentation](https://nf-co.re/cutandrun/usage) and don't hesitate to get in touch on the nf-core Slack [#cutandrun](https://nfcore.slack.com/channels/cutandrun) channel ([join our Slack here](https://nf-co.re/join/slack)). + +## Pipeline contribution conventions + +To make the nf-core/cutandrun code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. + +### Adding a new step + +If you wish to contribute a new step, please use the following coding standards: + +1. Define the corresponding input channel into your new process from the expected previous process channel +2. Write the process block (see below). +3. Define the output channel if needed (see below). +4. Add any new flags/options to `nextflow.config` with a default (see below). +5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`). +6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter). +7. Add sanity checks for all relevant parameters. +8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`. +9. Do local tests that the new code works properly and as expected. +10. Add a new test command in `.github/workflow/ci.yaml`. +11. If applicable add a [MultiQC](https://https://multiqc.info/) module. +12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order. +13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`. + +### Default values + +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`. + +### 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/%7B%7Bcookiecutter.name_noslash%7D%7D/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 `${task.cpu}` and `${task.memory}` variables in the `script:` block. + +### Naming schemes + +Please use the following naming schemes, to make it easy to understand what is going where. + +* initial process channel: `ch_output_from_` +* intermediate and terminal channels: `ch__for_` + +### 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]` + +### Software version reporting + +If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process. + +Add to the script block of the process, something like the following: + +```bash + --version &> v_.txt 2>&1 || true +``` + +or + +```bash + --help | head -n 1 &> v_.txt 2>&1 || true +``` + +You then need to edit the script `bin/scrape_software_versions.py` to: + +1. Add a Python regex for your tool's `--version` output (as in stored in the `v_.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1` +2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC. + +### Images and figures + +For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 00000000..ade74055 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,64 @@ +--- +name: Bug report +about: Report something that is broken or incorrect +labels: bug +--- + + + +## Check Documentation + +I have checked the following places for your error: + +- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) +- [ ] [nf-core/cutandrun pipeline documentation](https://nf-co.re/nf-core/cutandrun/usage) + +## Description of the bug + + + +## Steps to reproduce + +Steps to reproduce the behaviour: + +1. Command line: +2. See error: + +## Expected behaviour + + + +## Log files + +Have you provided the following extra information/files: + +- [ ] The command used to run the pipeline +- [ ] The `.nextflow.log` file + +## System + +- Hardware: +- Executor: +- OS: +- Version + +## Nextflow Installation + +- Version: + +## Container engine + +- Engine: +- version: +- Image tag: + +## Additional context + + diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..f78ab65d --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,8 @@ +blank_issues_enabled: false +contact_links: + - name: Join nf-core + url: https://nf-co.re/join + about: Please join the nf-core community here + - name: "Slack #cutandrun channel" + url: https://nfcore.slack.com/channels/cutandrun + about: Discussion about the nf-core/cutandrun pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 00000000..14a6c362 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,32 @@ +--- +name: Feature request +about: Suggest an idea for the nf-core website +labels: enhancement +--- + + + +## Is your feature request related to a problem? Please describe + + + + + +## Describe the solution you'd like + + + +## Describe alternatives you've considered + + + +## Additional context + + diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 00000000..07fee469 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,26 @@ + + +## PR checklist + +- [ ] This comment contains a description of changes (with reason). +- [ ] If you've fixed a bug or added code that should be tested, add tests! + - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py` + - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md) + - [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] Make sure your code lints (`nf-core lint .`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). +- [ ] Usage Documentation in `docs/usage.md` is updated. +- [ ] Output Documentation in `docs/output.md` is updated. +- [ ] `CHANGELOG.md` is updated. +- [ ] `README.md` is updated (including new tool citations and authors/contributors). diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml new file mode 100644 index 00000000..8d7eb53b --- /dev/null +++ b/.github/markdownlint.yml @@ -0,0 +1,12 @@ +# Markdownlint configuration file +default: true +line-length: false +no-duplicate-header: + siblings_only: true +no-inline-html: + allowed_elements: + - img + - p + - kbd + - details + - summary diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml new file mode 100644 index 00000000..efaab75a --- /dev/null +++ b/.github/workflows/awsfulltest.yml @@ -0,0 +1,43 @@ +name: nf-core AWS full size tests +# This workflow is triggered on published releases. +# It can be additionally triggered manually with GitHub actions workflow dispatch. +# It runs the -profile 'test_full' on AWS batch + +on: + workflow_run: + workflows: ["nf-core Docker push (release)"] + types: [completed] + workflow_dispatch: + +jobs: + run-awstest: + name: Run AWS full tests + if: github.repository == 'nf-core/cutandrun' + runs-on: ubuntu-latest + steps: + - name: Setup Miniconda + uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: 3.7 + - name: Install awscli + run: conda install -c conda-forge awscli + - name: Start AWS batch job + # TODO nf-core: You can customise AWS full pipeline tests as required + # Add full size test data (but still relatively small datasets for few samples) + # on the `test_full.config` test runs with only one set of parameters + # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command + env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} + AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} + AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} + AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} + run: | + aws batch submit-job \ + --region eu-west-1 \ + --job-name nf-core-cutandrun \ + --job-queue $AWS_JOB_QUEUE \ + --job-definition $AWS_JOB_DEFINITION \ + --container-overrides '{"command": ["nf-core/cutandrun", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/cutandrun/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/cutandrun/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml new file mode 100644 index 00000000..f19f98da --- /dev/null +++ b/.github/workflows/awstest.yml @@ -0,0 +1,39 @@ +name: nf-core AWS test +# This workflow is triggered on push to the master branch. +# It can be additionally triggered manually with GitHub actions workflow dispatch. +# It runs the -profile 'test' on AWS batch. + +on: + workflow_dispatch: + +jobs: + run-awstest: + name: Run AWS tests + if: github.repository == 'nf-core/cutandrun' + runs-on: ubuntu-latest + steps: + - name: Setup Miniconda + uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: 3.7 + - name: Install awscli + run: conda install -c conda-forge awscli + - name: Start AWS batch job + # 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 + env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} + AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} + AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} + AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} + run: | + aws batch submit-job \ + --region eu-west-1 \ + --job-name nf-core-cutandrun \ + --job-queue $AWS_JOB_QUEUE \ + --job-definition $AWS_JOB_DEFINITION \ + --container-overrides '{"command": ["nf-core/cutandrun", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/cutandrun/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/cutandrun/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml new file mode 100644 index 00000000..b6f858ba --- /dev/null +++ b/.github/workflows/branch.yml @@ -0,0 +1,37 @@ +name: nf-core branch protection +# This workflow is triggered on PRs to master branch on the repository +# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +on: + pull_request_target: + branches: [master] + +jobs: + test: + runs-on: ubuntu-latest + steps: + # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + - name: Check PRs + if: github.repository == 'nf-core/cutandrun' + run: | + { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/cutandrun ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + + + # If the above check failed, post a comment on the PR explaining the failure + # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v1 + with: + message: | + Hi @${{ github.event.pull_request.user.login }}, + + It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch. + The `master` branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch. + + You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 00000000..8a007c00 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,40 @@ +name: nf-core CI +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors +on: + push: + branches: + - dev + pull_request: + release: + types: [published] + +jobs: + test: + name: Run workflow tests + # Only run on push if this is the nf-core dev branch (merged PRs) + if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }} + runs-on: ubuntu-latest + env: + NXF_VER: ${{ matrix.nxf_ver }} + NXF_ANSI_LOG: false + strategy: + matrix: + # Nextflow versions: check pipeline minimum and current latest + nxf_ver: [20.11.0-edge] + steps: + - name: Check out pipeline code + uses: actions/checkout@v2 + + - name: Install Nextflow + env: + CAPSULE_LOG: none + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Run pipeline with test data + # 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 diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 00000000..bef81e61 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,77 @@ +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 that the code meets the nf-core guidelines +on: + push: + pull_request: + release: + types: [published] + +jobs: + Markdown: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-node@v1 + with: + node-version: '10' + - name: Install markdownlint + run: npm install -g markdownlint-cli + - name: Run Markdownlint + run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml + YAML: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v1 + - uses: actions/setup-node@v1 + with: + node-version: '10' + - name: Install yaml-lint + run: npm install -g yaml-lint + - name: Run yaml-lint + run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml") + nf-core: + runs-on: ubuntu-latest + steps: + + - name: Check out pipeline code + uses: actions/checkout@v2 + + - name: Install Nextflow + env: + CAPSULE_LOG: none + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - uses: actions/setup-python@v1 + with: + python-version: '3.6' + architecture: 'x64' + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install nf-core + + - name: Run nf-core lint + 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 ${GITHUB_WORKSPACE} --markdown lint_results.md + + - name: Save PR number + if: ${{ always() }} + run: echo ${{ github.event.pull_request.number }} > PR_number.txt + + - name: Upload linting log file artifact + if: ${{ always() }} + uses: actions/upload-artifact@v2 + with: + name: linting-log-file + path: | + lint_log.txt + lint_results.md + PR_number.txt + diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml new file mode 100644 index 00000000..90f03c6f --- /dev/null +++ b/.github/workflows/linting_comment.yml @@ -0,0 +1,29 @@ + +name: nf-core linting comment +# This workflow is triggered after the linting action is complete +# It posts an automated comment to the PR, even if the PR is coming from a fork + +on: + workflow_run: + workflows: ["nf-core linting"] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - name: Download lint results + uses: dawidd6/action-download-artifact@v2 + with: + workflow: linting.yml + + - name: Get PR number + id: pr_number + run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)" + + - name: Post PR comment + uses: marocchino/sticky-pull-request-comment@v2 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.pr_number.outputs.pr_number }} + path: linting-logs/lint_results.md + diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000..aa4bb5b3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,9 @@ +.nextflow* +work/ +data/ +results/ +.DS_Store +tests/ +testing/ +testing* +*.pyc diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..c4db519a --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,16 @@ +# nf-core/cutandrun: Changelog + +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). + +## [1.0dev] - [date] + +Initial release of nf-core/cutandrun, created with the [nf-core](https://nf-co.re/) template. + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` diff --git a/CITATIONS.md b/CITATIONS.md new file mode 100644 index 00000000..f664f7f6 --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1,32 @@ +# nf-core/cutandrun: Citations + +## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) + +> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. + +## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) + +> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. + +## Pipeline tools + +* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + +* [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. + +## Software packaging/containerisation tools + +* [Anaconda](https://anaconda.com) + > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. + +* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) + > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. + +* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) + > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. + +* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + +* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..405fb1bf --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,46 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version] + +[homepage]: https://contributor-covenant.org +[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/ diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..40528b68 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) Chris Cheshire and Charlotte West + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 00000000..f5c72ede --- /dev/null +++ b/README.md @@ -0,0 +1,93 @@ +# ![nf-core/cutandrun](docs/images/nf-core-cutandrun_logo.png) + +[![GitHub Actions CI Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+linting%22) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/cutandrun/results) +[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A520.11.0--edge-23aa62.svg?labelColor=000000)](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/) + +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23cutandrun-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/cutandrun) +[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) +[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) + +## Introduction + + +**nf-core/cutandrun** is a bioinformatics best-practise analysis pipeline for + +The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. + + +On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/cutandrun/results). + +## Pipeline summary + + + +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) + +## Quick Start + +1. Install [`nextflow`](https://nf-co.re/usage/installation) + +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ + +3. Download the pipeline and test it on a minimal dataset with a single command: + + ```bash + nextflow run nf-core/cutandrun -profile test, + ``` + + > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. + > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. It is also highly recommended to use the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) settings to store the images in a central location for future pipeline runs. + > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + +4. Start running your own analysis! + + + + ```bash + nextflow run nf-core/cutandrun -profile --input samplesheet.csv --genome GRCh37 + ``` + +See [usage docs](https://nf-co.re/cutandrun/usage) for all of the available options when running the pipeline. + +## Documentation + +The nf-core/cutandrun pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/cutandrun/usage) and [output](https://nf-co.re/cutandrun/output). + +## Credits + +nf-core/cutandrun was originally written by Chris Cheshire and Charlotte West. + +We thank the following people for their extensive assistance in the development +of this pipeline: + + + +## Contributions and Support + +If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). + +For further information or help, don't hesitate to get in touch on the [Slack `#cutandrun` channel](https://nfcore.slack.com/channels/cutandrun) (you can join with [this invite](https://nf-co.re/join/slack)). + +## Citations + + + + + +An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. + +You can cite the `nf-core` publication as follows: + +> **The nf-core framework for community-curated bioinformatics pipelines.** +> +> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. +> +> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). diff --git a/assets/email_template.html b/assets/email_template.html new file mode 100644 index 00000000..0e691c4f --- /dev/null +++ b/assets/email_template.html @@ -0,0 +1,54 @@ + + + + + + + + + nf-core/cutandrun Pipeline Report + + +
+ + + +

nf-core/cutandrun v${version}

+

Run Name: $runName

+ +<% if (!success){ + out << """ +
+

nf-core/cutandrun execution completed unsuccessfully!

+

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

+

The full error message was:

+ 
${errorReport}
+
+ """ +} else { + out << """ +
+ nf-core/cutandrun execution completed successfully! +
+ """ +} +%> + +

The workflow was completed at $dateComplete (duration: $duration)

+

The command used to launch the workflow was as follows:

+
$commandLine
+ +

Pipeline Configuration:

+ + + <% out << summary.collect{ k,v -> "" }.join("\n") %> + +
$k
$v
+ +

nf-core/cutandrun

+

https://github.com/nf-core/cutandrun

+ +
+ + + diff --git a/assets/email_template.txt b/assets/email_template.txt new file mode 100644 index 00000000..d34cf2af --- /dev/null +++ b/assets/email_template.txt @@ -0,0 +1,40 @@ +---------------------------------------------------- + ,--./,-. + ___ __ __ __ ___ /,-._.--~\\ + |\\ | |__ __ / ` / \\ |__) |__ } { + | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, + `._,._,' + nf-core/cutandrun v${version} +---------------------------------------------------- + +Run Name: $runName + +<% if (success){ + out << "## nf-core/cutandrun execution completed successfully! ##" +} else { + out << """#################################################### +## nf-core/cutandrun execution completed unsuccessfully! ## +#################################################### +The exit status of the task that caused the workflow execution to fail was: $exitStatus. +The full error message was: + +${errorReport} +""" +} %> + + +The workflow was completed at $dateComplete (duration: $duration) + +The command used to launch the workflow was as follows: + + $commandLine + + + +Pipeline Configuration: +----------------------- +<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> + +-- +nf-core/cutandrun +https://github.com/nf-core/cutandrun diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml new file mode 100644 index 00000000..bc24430e --- /dev/null +++ b/assets/multiqc_config.yaml @@ -0,0 +1,11 @@ +report_comment: > + This report has been generated by the nf-core/cutandrun + analysis pipeline. For information about how to interpret these results, please see the + documentation. +report_section_order: + software_versions: + order: -1000 + nf-core-cutandrun-summary: + order: -1001 + +export_plots: true diff --git a/assets/nf-core-cutandrun_logo.png b/assets/nf-core-cutandrun_logo.png new file mode 100644 index 00000000..8d24fe55 Binary files /dev/null and b/assets/nf-core-cutandrun_logo.png differ diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv new file mode 100644 index 00000000..cd5a39a0 --- /dev/null +++ b/assets/samplesheet.csv @@ -0,0 +1,8 @@ +group,replicate,fastq_1,fastq_2 +control,1,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz +control,2,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz +control,3,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz +treatment,1,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, +treatment,2,/path/to/fastq/files/AEG588A5_S5_L003_R1_001.fastq.gz, +treatment,3,/path/to/fastq/files/AEG588A6_S6_L003_R1_001.fastq.gz, +treatment,3,/path/to/fastq/files/AEG588A6_S6_L004_R1_001.fastq.gz, diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt new file mode 100644 index 00000000..cf377e8f --- /dev/null +++ b/assets/sendmail_template.txt @@ -0,0 +1,53 @@ +To: $email +Subject: $subject +Mime-Version: 1.0 +Content-Type: multipart/related;boundary="nfcoremimeboundary" + +--nfcoremimeboundary +Content-Type: text/html; charset=utf-8 + +$email_html + +--nfcoremimeboundary +Content-Type: image/png;name="nf-core-cutandrun_logo.png" +Content-Transfer-Encoding: base64 +Content-ID: +Content-Disposition: inline; filename="nf-core-cutandrun_logo.png" + +<% out << new File("$projectDir/assets/nf-core-cutandrun_logo.png"). + bytes. + encodeBase64(). + toString(). + tokenize( '\n' )*. + toList()*. + collate( 76 )*. + collect { it.join() }. + flatten(). + join( '\n' ) %> + +<% +if (mqcFile){ +def mqcFileObj = new File("$mqcFile") +if (mqcFileObj.length() < mqcMaxSize){ +out << """ +--nfcoremimeboundary +Content-Type: text/html; name=\"multiqc_report\" +Content-Transfer-Encoding: base64 +Content-ID: +Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" + +${mqcFileObj. + bytes. + encodeBase64(). + toString(). + tokenize( '\n' )*. + toList()*. + collate( 76 )*. + collect { it.join() }. + flatten(). + join( '\n' )} +""" +}} +%> + +--nfcoremimeboundary-- diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py new file mode 100755 index 00000000..0b317500 --- /dev/null +++ b/bin/check_samplesheet.py @@ -0,0 +1,169 @@ +#!/usr/bin/env python + +# TODO nf-core: Update the script to check the samplesheet +# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv + + +import os +import sys +import errno +import argparse + + +def parse_args(args=None): + Description = "Reformat nf-core/cutandrun samplesheet file and check its contents." + Epilog = "Example usage: python check_samplesheet.py " + + parser = argparse.ArgumentParser(description=Description, epilog=Epilog) + parser.add_argument("FILE_IN", help="Input samplesheet file.") + parser.add_argument("FILE_OUT", help="Output file.") + return parser.parse_args(args) + + +def make_dir(path): + if len(path) > 0: + try: + os.makedirs(path) + except OSError as exception: + if exception.errno != errno.EEXIST: + raise exception + + +def print_error(error, context="Line", context_str=""): + error_str = "ERROR: Please check samplesheet -> {}".format(error) + if context != "" and context_str != "": + error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format( + error, context.strip(), context_str.strip() + ) + print(error_str) + sys.exit(1) + + +# TODO nf-core: Update the check_samplesheet function +def check_samplesheet(file_in, file_out): + """ + This function checks that the samplesheet follows the following structure: + + group,replicate,fastq_1,fastq_2 + WT,1,WT_LIB1_REP1_1.fastq.gz,WT_LIB1_REP1_2.fastq.gz + WT,1,WT_LIB2_REP1_1.fastq.gz,WT_LIB2_REP1_2.fastq.gz + WT,2,WT_LIB1_REP2_1.fastq.gz,WT_LIB1_REP2_2.fastq.gz + KO,1,KO_LIB1_REP1_1.fastq.gz,KO_LIB1_REP1_2.fastq.gz + """ + + sample_run_dict = {} + with open(file_in, "r") as fin: + + ## Check header + MIN_COLS = 3 + # TODO nf-core: Update the column names for the input samplesheet + HEADER = ["group", "replicate", "fastq_1", "fastq_2"] + header = [x.strip('"') for x in fin.readline().strip().split(",")] + if header[: len(HEADER)] != HEADER: + print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER))) + sys.exit(1) + + ## Check sample entries + for line in fin: + lspl = [x.strip().strip('"') for x in line.strip().split(",")] + + ## Check valid number of columns per row + if len(lspl) < len(HEADER): + print_error( + "Invalid number of columns (minimum = {})!".format(len(HEADER)), + "Line", + line, + ) + num_cols = len([x for x in lspl if x]) + if num_cols < MIN_COLS: + print_error( + "Invalid number of populated columns (minimum = {})!".format(MIN_COLS), + "Line", + line, + ) + + ## Check sample name entries + sample, replicate, fastq_1, fastq_2 = lspl[: len(HEADER)] + if sample: + if sample.find(" ") != -1: + print_error("Group entry contains spaces!", "Line", line) + else: + print_error("Group entry has not been specified!", "Line", line) + + ## Check replicate entry is integer + if not replicate.isdigit(): + print_error("Replicate id not an integer!", "Line", line) + replicate = int(replicate) + + ## Check FastQ file extension + for fastq in [fastq_1, fastq_2]: + if fastq: + if fastq.find(" ") != -1: + print_error("FastQ file contains spaces!", "Line", line) + if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"): + print_error( + "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!", + "Line", + line, + ) + + ## Auto-detect paired-end/single-end + sample_info = [] ## [single_end, fastq_1, fastq_2] + if sample and fastq_1 and fastq_2: ## Paired-end short reads + sample_info = ["0", fastq_1, fastq_2] + elif sample and fastq_1 and not fastq_2: ## Single-end short reads + sample_info = ["1", fastq_1, fastq_2] + else: + print_error("Invalid combination of columns provided!", "Line", line) + ## Create sample mapping dictionary = {sample: {replicate : [ single_end, fastq_1, fastq_2 ]}} + if sample not in sample_run_dict: + sample_run_dict[sample] = {} + if replicate not in sample_run_dict[sample]: + sample_run_dict[sample][replicate] = [sample_info] + else: + if sample_info in sample_run_dict[sample][replicate]: + print_error("Samplesheet contains duplicate rows!", "Line", line) + else: + sample_run_dict[sample][replicate].append(sample_info) + + ## Write validated samplesheet with appropriate columns + if len(sample_run_dict) > 0: + out_dir = os.path.dirname(file_out) + make_dir(out_dir) + with open(file_out, "w") as fout: + + fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n") + for sample in sorted(sample_run_dict.keys()): + + ## Check that replicate ids are in format 1.. + uniq_rep_ids = set(sample_run_dict[sample].keys()) + if len(uniq_rep_ids) != max(uniq_rep_ids): + print_error( + "Replicate ids must start with 1..!", + "Group", + sample, + ) + for replicate in sorted(sample_run_dict[sample].keys()): + + ## Check that multiple runs of the same sample are of the same datatype + if not all( + x[0] == sample_run_dict[sample][replicate][0][0] for x in sample_run_dict[sample][replicate] + ): + print_error( + "Multiple runs of a sample must be of the same datatype!", + "Group", + sample, + ) + ## Write to file + for idx, sample_info in enumerate(sample_run_dict[sample][replicate]): + sample_id = "{}_R{}_T{}".format(sample, replicate, idx + 1) + fout.write(",".join([sample_id] + sample_info) + "\n") + + +def main(args=None): + args = parse_args(args) + check_samplesheet(args.FILE_IN, args.FILE_OUT) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py new file mode 100755 index 00000000..155177ac --- /dev/null +++ b/bin/scrape_software_versions.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python +from __future__ import print_function +import os + +results = {} +version_files = [x for x in os.listdir(".") if x.endswith(".version.txt")] +for version_file in version_files: + + software = version_file.replace(".version.txt", "") + if software == "pipeline": + software = "nf-core/cutandrun" + + with open(version_file) as fin: + version = fin.read().strip() + results[software] = version + +# Dump to YAML +print( + """ +id: 'software_versions' +section_name: 'nf-core/cutandrun Software Versions' +section_href: 'https://github.com/nf-core/cutandrun' +plot_type: 'html' +description: 'are collected at run time from the software output.' +data: | +
+""" +) +for k, v in sorted(results.items()): + print("
{}
{}
".format(k, v)) +print("
") + +# Write out regexes as csv file: +with open("software_versions.csv", "w") as f: + for k, v in sorted(results.items()): + f.write("{}\t{}\n".format(k, v)) diff --git a/conf/base.config b/conf/base.config new file mode 100644 index 00000000..12873596 --- /dev/null +++ b/conf/base.config @@ -0,0 +1,55 @@ +/* + * ------------------------------------------------- + * nf-core/cutandrun Nextflow base config file + * ------------------------------------------------- + * A 'blank slate' config file, appropriate for general + * use on most high performace compute environments. + * Assumes that all software is installed and available + * on the PATH. Runs in `local` mode - all jobs will be + * run on the logged in environment. + */ + +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' ) } + + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + maxRetries = 1 + maxErrors = '-1' + + // Process-specific resource requirements + // NOTE - Please try and re-use the labels below as much as possible. + // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. + // If possible, it would be nice to keep the same label naming convention when + // adding in your local modules too. + // TODO nf-core: Customise requirements for specific processes. + // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors + 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' ) } + } + 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' ) } + } + 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' ) } + } + withLabel:process_long { + time = { check_max( 20.h * task.attempt, 'time' ) } + } + withLabel:error_ignore { + errorStrategy = 'ignore' + } + withLabel:error_retry { + errorStrategy = 'retry' + maxRetries = 2 + } +} diff --git a/conf/igenomes.config b/conf/igenomes.config new file mode 100644 index 00000000..7485867b --- /dev/null +++ b/conf/igenomes.config @@ -0,0 +1,420 @@ +/* + * ------------------------------------------------- + * Nextflow config file for iGenomes paths + * ------------------------------------------------- + * Defines reference genomes, using iGenome paths + * Can be used by any config that customises the base + * path using $params.igenomes_base / --igenomes_base + */ + +params { + // illumina iGenomes reference file paths + genomes { + 'GRCh37' { + fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" + } + 'GRCh38' { + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + } + 'GRCm38' { + fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "1.87e9" + blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" + } + 'TAIR10' { + fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" + mito_name = "Mt" + } + 'EB2' { + fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" + } + 'UMD3.1' { + fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" + mito_name = "MT" + } + 'WBcel235' { + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" + mito_name = "MtDNA" + macs_gsize = "9e7" + } + 'CanFam3.1' { + fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" + mito_name = "MT" + } + 'GRCz10' { + fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'BDGP6' { + fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" + mito_name = "M" + macs_gsize = "1.2e8" + } + 'EquCab2' { + fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" + mito_name = "MT" + } + 'EB1' { + fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" + } + 'Galgal4' { + fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'Gm01' { + fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" + } + 'Mmul_1' { + fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" + mito_name = "MT" + } + 'IRGSP-1.0' { + fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" + mito_name = "Mt" + } + 'CHIMP2.1.4' { + fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" + mito_name = "MT" + } + 'Rnor_6.0' { + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'R64-1-1' { + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" + mito_name = "MT" + macs_gsize = "1.2e7" + } + 'EF2' { + fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "1.21e7" + } + 'Sbi1' { + fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" + } + 'Sscrofa10.2' { + fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" + mito_name = "MT" + } + 'AGPv3' { + fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" + mito_name = "Mt" + } + 'hg38' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + } + 'hg19' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" + } + 'mm10' { + fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "1.87e9" + blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" + } + 'bosTau8' { + fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + 'ce10' { + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "9e7" + } + 'canFam3' { + fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" + mito_name = "chrM" + } + 'danRer10' { + fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + 'dm6' { + fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "1.2e8" + } + 'equCab2' { + fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" + mito_name = "chrM" + } + 'galGal4' { + fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" + mito_name = "chrM" + } + 'panTro4' { + fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" + mito_name = "chrM" + } + 'rn6' { + fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + 'sacCer3' { + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" + readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "1.2e7" + } + 'susScr3' { + fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/" + bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" + mito_name = "chrM" + } + } +} diff --git a/conf/modules.config b/conf/modules.config new file mode 100644 index 00000000..f26191e0 --- /dev/null +++ b/conf/modules.config @@ -0,0 +1,28 @@ +/* + * -------------------------------------------------- + * Config file for defining DSL2 per module options + * -------------------------------------------------- + * + * Available keys to override module options: + * args = Additional arguments appended to command in module. + * args2 = Second set of arguments appended to command in module (multi-tool modules). + * publish_dir = Directory to publish results. + * publish_by_id = Publish results in separate folders by meta.id value. + * publish_files = Groovy map where key = "file_ext" and value = "directory" to publish results for that file extension + * The value of "directory" is appended to the standard "publish_dir" path as defined above. + * If publish_files == null (unspecified) - All files are published. + * If publish_files == false - No files are published. + * suffix = File name suffix for output files. + * + */ + +params { + modules { + 'fastqc' { + args = "--quiet" + } + 'multiqc' { + args = "" + } + } +} diff --git a/conf/test.config b/conf/test.config new file mode 100644 index 00000000..e1ed861e --- /dev/null +++ b/conf/test.config @@ -0,0 +1,26 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running tests + * ------------------------------------------------- + * Defines bundled input files and everything required + * to run a fast and simple test. Use as follows: + * nextflow run nf-core/cutandrun -profile test, + */ + +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 + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv' + + // Genome references + genome = 'R64-1-1' +} diff --git a/conf/test_full.config b/conf/test_full.config new file mode 100644 index 00000000..85b58b87 --- /dev/null +++ b/conf/test_full.config @@ -0,0 +1,21 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running full-size tests + * ------------------------------------------------- + * Defines bundled input files and everything required + * to run a full size pipeline test. Use as follows: + * nextflow run nf-core/cutandrun -profile test_full, + */ + +params { + config_profile_name = 'Full test profile' + config_profile_description = 'Full test dataset to check pipeline function' + + // Input data for full size test + // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) + // TODO nf-core: Give any required params for the test so that command line flags are not needed + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design_full.csv' + + // Genome references + genome = 'GRCh37' +} diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 00000000..a0c1cc8a --- /dev/null +++ b/docs/README.md @@ -0,0 +1,10 @@ +# nf-core/cutandrun: Documentation + +The nf-core/cutandrun documentation is split into the following pages: + +* [Usage](usage.md) + * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. +* [Output](output.md) + * An overview of the different results produced by the pipeline and how to interpret them. + +You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png new file mode 100755 index 00000000..361d0e47 Binary files /dev/null and b/docs/images/mqc_fastqc_adapter.png differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png new file mode 100755 index 00000000..cb39ebb8 Binary files /dev/null and b/docs/images/mqc_fastqc_counts.png differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png new file mode 100755 index 00000000..a4b89bf5 Binary files /dev/null and b/docs/images/mqc_fastqc_quality.png differ diff --git a/docs/images/nf-core-cutandrun_logo.png b/docs/images/nf-core-cutandrun_logo.png new file mode 100644 index 00000000..8d24fe55 Binary files /dev/null and b/docs/images/nf-core-cutandrun_logo.png differ diff --git a/docs/output.md b/docs/output.md new file mode 100644 index 00000000..c004a930 --- /dev/null +++ b/docs/output.md @@ -0,0 +1,74 @@ +# nf-core/cutandrun: Output + +## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/cutandrun/output](https://nf-co.re/cutandrun/output) + +> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ + +## Introduction + +This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. + +The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. + + + +## Pipeline overview + +The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: + +* [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 + +
+Output files + +* `fastqc/` + * `*_fastqc.html`: FastQC report containing quality metrics for your untrimmed raw fastq files. + * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. + +> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. To see how your reads look after adapter and quality trimming please refer to the FastQC reports in the `trimgalore/fastqc/` directory. + +
+ +[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) + +> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. + +### MultiQC + +
+Output files + +* `multiqc/` + * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. + * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. + * `multiqc_plots/`: directory containing static images from the report in various formats. + +
+ +[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. + +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . + +### Pipeline information + +
+Output files + +* `pipeline_info/` + * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. + * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`. + * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. + +
+ +[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/docs/usage.md b/docs/usage.md new file mode 100644 index 00000000..cb9846fb --- /dev/null +++ b/docs/usage.md @@ -0,0 +1,183 @@ +# nf-core/cutandrun: Usage + +## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/cutandrun/usage](https://nf-co.re/cutandrun/usage) + +> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ + +## Introduction + + + +## Samplesheet input + +You will need to create a samplesheet file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. + +```bash +--input '[path to samplesheet file]' +``` + +### Multiple replicates + +The `group` identifier is the same when you have multiple replicates from the same experimental group, just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1. Below is an example for a single experimental group in triplicate: + +```bash +group,replicate,fastq_1,fastq_2 +control,1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz +control,2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz +control,3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz +``` + +### Multiple runs of the same library + +The `group` and `replicate` identifiers are the same when you have re-sequenced the same sample more than once (e.g. to increase sequencing depth). The pipeline will concatenate the raw reads before alignment. Below is an example for two samples sequenced across multiple lanes: + +```bash +group,replicate,fastq_1,fastq_2 +control,1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz +control,1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz +treatment,1,AEG588A4_S4_L003_R1_001.fastq.gz,AEG588A4_S4_L003_R2_001.fastq.gz +treatment,1,AEG588A4_S4_L004_R1_001.fastq.gz,AEG588A4_S4_L004_R2_001.fastq.gz +``` + +### Full design + +A final design file consisting of both single- and paired-end data may look something like the one below. This is for two experimental groups in triplicate, where the last replicate of the `treatment` group has been sequenced twice. + +```bash +group,replicate,fastq_1,fastq_2 +control,1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz +control,2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz +control,3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz +treatment,1,AEG588A4_S4_L003_R1_001.fastq.gz, +treatment,2,AEG588A5_S5_L003_R1_001.fastq.gz, +treatment,3,AEG588A6_S6_L003_R1_001.fastq.gz, +treatment,3,AEG588A6_S6_L004_R1_001.fastq.gz, +``` + +| Column | Description | +|----------------|-------------------------------------------------------------------------------------------------------------| +| `group` | Group identifier for sample. This will be identical for replicate samples from the same experimental group. | +| `replicate` | Integer representing replicate number. Must start from `1..`. | +| `fastq_1` | Full path to FastQ file for read 1. File has to be zipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for read 2. File has to be zipped and have the extension ".fastq.gz" or ".fq.gz". | + +An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. + +## Running the pipeline + +The typical command for running the pipeline is as follows: + +```bash +nextflow run nf-core/cutandrun --input samplesheet.csv -profile docker +``` + +This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. + +Note that the pipeline will create the following files in your working directory: + +```bash +work # Directory containing the nextflow working files +results # Finished results (configurable, see below) +.nextflow_log # Log file from Nextflow +# Other nextflow hidden files, eg. history of pipeline runs and old logs. +``` + +### Updating the pipeline + +When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: + +```bash +nextflow pull nf-core/cutandrun +``` + +### Reproducibility + +It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. + +First, go to the [nf-core/cutandrun releases page](https://github.com/nf-core/cutandrun/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. + +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. + +## Core Nextflow arguments + +> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). + +### `-profile` + +Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. + +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Conda) - see below. + +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. + +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). + +Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! +They are loaded in sequence, so later profiles can overwrite earlier profiles. + +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended. + +* `docker` + * A generic configuration profile to be used with [Docker](https://docker.com/) + * Pulls software from Docker Hub: [`nfcore/cutandrun`](https://hub.docker.com/r/nfcore/cutandrun/) +* `singularity` + * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) + * Pulls software from Docker Hub: [`nfcore/cutandrun`](https://hub.docker.com/r/nfcore/cutandrun/) +* `podman` + * A generic configuration profile to be used with [Podman](https://podman.io/) + * Pulls software from Docker Hub: [`nfcore/cutandrun`](https://hub.docker.com/r/nfcore/cutandrun/) +* `conda` + * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity or Podman. + * A generic configuration profile to be used with [Conda](https://conda.io/docs/) + * Pulls most software from [Bioconda](https://bioconda.github.io/) +* `test` + * A profile with a complete configuration for automated testing + * Includes links to test data so needs no other parameters + +### `-resume` + +Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. + +You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names. + +### `-c` + +Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information. + +#### Custom resource requests + +Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped. + +Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config: + +```nextflow +process { + withName: star { + memory = 32.GB + } +} +``` + +See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information. + +If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition above). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. + +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). + +### Running in the background + +Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. + +The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file. + +Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time. +Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs). + +#### Nextflow memory requirements + +In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. +We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): + +```bash +NXF_OPTS='-Xms1g -Xmx4g' +``` diff --git a/lib/Checks.groovy b/lib/Checks.groovy new file mode 100644 index 00000000..16747ed8 --- /dev/null +++ b/lib/Checks.groovy @@ -0,0 +1,101 @@ +/* + * This file holds several functions used to perform standard checks for the nf-core pipeline template. + */ + +import org.yaml.snakeyaml.Yaml + +class Checks { + + static void check_conda_channels(log) { + Yaml parser = new Yaml() + def channels = [] + 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 + } + + // Check that all channels are present + def required_channels = ['conda-forge', 'bioconda', 'defaults'] + def conda_check_failed = !required_channels.every { ch -> ch in channels } + + // Check that they are in the right order + conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda')) + conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults')) + + if (conda_check_failed) { + 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/user/install.html#set-up-channels\n" + + " NB: The order of the channels matters!\n" + + "===================================================================================" + } + } + + static void aws_batch(workflow, params) { + if (workflow.profile.contains('awsbatch')) { + assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" + // Check outdir paths to be S3 buckets if running on AWSBatch + // related: https://github.com/nextflow-io/nextflow/issues/813 + assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" + // Prevent trace files to be stored on S3 since S3 does not support rolling files. + assert !params.tracedir.startsWith('s3:') : "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles." + } + } + + static void hostname(workflow, params, log) { + Map colors = Headers.log_colours(params.monochrome_logs) + if (params.hostnames) { + def hostname = "hostname".execute().text.trim() + params.hostnames.each { prof, hnames -> + hnames.each { hname -> + if (hostname.contains(hname) && !workflow.profile.contains(prof)) { + log.info "=${colors.yellow}====================================================${colors.reset}=\n" + + "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" + + " but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" + + " ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" + + "=${colors.yellow}====================================================${colors.reset}=" + } + } + } + } + } + + // Citation string + private static String citation(workflow) { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " https://doi.org/10.5281/zenodo.1400710\n\n" + + "* The nf-core framework\n" + + " https://dx.doi.org/10.1038/s41587-020-0439-x\n" + + " https://rdcu.be/b1GjZ\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + } + + // Exit pipeline if incorrect --genome key provided + static void genome_exists(params, log) { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + log.error "=============================================================================\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "=============================================================================" + System.exit(0) + } + } + + // Get attribute from genome config file e.g. fasta + static String get_genome_attribute(params, attribute) { + def val = '' + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + val = params.genomes[ params.genome ][ attribute ] + } + } + return val + } +} diff --git a/lib/Completion.groovy b/lib/Completion.groovy new file mode 100644 index 00000000..e745c986 --- /dev/null +++ b/lib/Completion.groovy @@ -0,0 +1,127 @@ +/* + * Functions to be run on completion of pipeline + */ + +class Completion { + static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = workflow.manifest.version + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = null + try { + if (workflow.success && !params.skip_multiqc) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + + // Check if we are only sending emails on failure + def email_address = params.email + if (!params.email && params.email_on_fail && !workflow.success) { + email_address = params.email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("$projectDir/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("$projectDir/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] + def sf = new File("$projectDir/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = Headers.log_colours(params.monochrome_logs) + if (email_address) { + try { + if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + mail_cmd += [ '-A', mqc_report ] + } + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_d = new File("${params.outdir}/pipeline_info/") + if (!output_d.exists()) { + output_d.mkdirs() + } + def output_hf = new File(output_d, "pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + def output_tf = new File(output_d, "pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + } + + static void summary(workflow, params, log) { + Map colors = Headers.log_colours(params.monochrome_logs) + 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.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + Checks.hostname(workflow, params, log) + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + } +} \ No newline at end of file diff --git a/lib/Headers.groovy b/lib/Headers.groovy new file mode 100644 index 00000000..15d1d388 --- /dev/null +++ b/lib/Headers.groovy @@ -0,0 +1,43 @@ +/* + * This file holds several functions used to render the nf-core ANSI header. + */ + +class Headers { + + private static Map log_colours(Boolean monochrome_logs) { + Map colorcodes = [:] + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['yellow_bold'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['red'] = monochrome_logs ? '' : "\033[1;91m" + return colorcodes + } + + static String dashed_line(monochrome_logs) { + Map colors = log_colours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" + } + + static String nf_core(workflow, monochrome_logs) { + Map colors = log_colours(monochrome_logs) + String.format( + """\n + ${dashed_line(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset} + ${dashed_line(monochrome_logs)} + """.stripIndent() + ) + } +} diff --git a/lib/Schema.groovy b/lib/Schema.groovy new file mode 100644 index 00000000..c2cad355 --- /dev/null +++ b/lib/Schema.groovy @@ -0,0 +1,228 @@ +/* + * This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. + */ + +import groovy.json.JsonSlurper + +class Schema { + /* + * This method tries to read a JSON params file + */ + private static LinkedHashMap params_load(String json_schema) { + def params_map = new LinkedHashMap() + try { + params_map = params_read(json_schema) + } catch (Exception e) { + println "Could not read parameters settings from JSON. $e" + params_map = new LinkedHashMap() + } + return params_map + } + + /* + Method to actually read in JSON file using Groovy. + Group (as Key), values are all parameters + - Parameter1 as Key, Description as Value + - Parameter2 as Key, Description as Value + .... + Group + - + */ + private static LinkedHashMap params_read(String json_schema) throws Exception { + def json = new File(json_schema).text + def Map json_params = (Map) new JsonSlurper().parseText(json).get('definitions') + /* Tree looks like this in nf-core schema + * definitions <- this is what the first get('definitions') gets us + group 1 + title + description + properties + parameter 1 + type + description + parameter 2 + type + description + group 2 + title + description + properties + parameter 1 + type + description + */ + def params_map = new LinkedHashMap() + json_params.each { key, val -> + def Map group = json_params."$key".properties // Gets the property object of the group + def title = json_params."$key".title + def sub_params = new LinkedHashMap() + group.each { innerkey, value -> + sub_params.put(innerkey, value) + } + params_map.put(title, sub_params) + } + return params_map + } + + /* + * Get maximum number of characters across all parameter names + */ + private static Integer params_max_chars(params_map) { + Integer max_chars = 0 + for (group in params_map.keySet()) { + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (param.size() > max_chars) { + max_chars = param.size() + } + } + } + return max_chars + } + + /* + * Beautify parameters for --help + */ + private static String params_help(workflow, params, json_schema, command) { + String output = Headers.nf_core(workflow, params.monochrome_logs) + "\n" + output += "Typical pipeline command:\n\n" + output += " ${command}\n\n" + def params_map = params_load(json_schema) + def max_chars = params_max_chars(params_map) + 1 + for (group in params_map.keySet()) { + output += group + "\n" + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + def type = "[" + group_params.get(param).type + "]" + def description = group_params.get(param).description + output += " \u001B[1m--" + param.padRight(max_chars) + "\u001B[1m" + type.padRight(10) + description + "\n" + } + output += "\n" + } + output += Headers.dashed_line(params.monochrome_logs) + output += "\n\n" + Checks.citation(workflow) + output += "\n\n" + Headers.dashed_line(params.monochrome_logs) + return output + } + + /* + * Groovy Map summarising parameters/workflow options used by the pipeline + */ + private static LinkedHashMap params_summary_map(workflow, params, json_schema) { + // Get a selection of core Nextflow workflow options + def Map workflow_summary = [:] + if (workflow.revision) { + workflow_summary['revision'] = workflow.revision + } + workflow_summary['runName'] = workflow.runName + if (workflow.containerEngine) { + workflow_summary['containerEngine'] = "$workflow.containerEngine" + } + if (workflow.container) { + workflow_summary['container'] = "$workflow.container" + } + workflow_summary['launchDir'] = workflow.launchDir + workflow_summary['workDir'] = workflow.workDir + workflow_summary['projectDir'] = workflow.projectDir + workflow_summary['userName'] = workflow.userName + workflow_summary['profile'] = workflow.profile + workflow_summary['configFiles'] = workflow.configFiles.join(', ') + + // Get pipeline parameters defined in JSON Schema + def Map params_summary = [:] + def blacklist = ['hostnames'] + def params_map = params_load(json_schema) + for (group in params_map.keySet()) { + def sub_params = new LinkedHashMap() + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (params.containsKey(param) && !blacklist.contains(param)) { + def params_value = params.get(param) + def schema_value = group_params.get(param).default + def param_type = group_params.get(param).type + if (schema_value == null) { + if (param_type == 'boolean') { + schema_value = false + } + if (param_type == 'string') { + schema_value = '' + } + if (param_type == 'integer') { + schema_value = 0 + } + } else { + if (param_type == 'string') { + if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { + def sub_string = schema_value.replace('\$projectDir','') + sub_string = sub_string.replace('\${projectDir}','') + if (params_value.contains(sub_string)) { + schema_value = params_value + } + } + if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { + def sub_string = schema_value.replace('\$params.outdir','') + sub_string = sub_string.replace('\${params.outdir}','') + if ("${params.outdir}${sub_string}" == params_value) { + schema_value = params_value + } + } + } + } + + if (params_value != schema_value) { + sub_params.put("$param", params_value) + } + } + } + params_summary.put(group, sub_params) + } + return [ 'Core Nextflow options' : workflow_summary ] << params_summary + } + + /* + * Beautify parameters for summary and return as string + */ + private static String params_summary_log(workflow, params, json_schema) { + String output = Headers.nf_core(workflow, params.monochrome_logs) + "\n" + def params_map = params_summary_map(workflow, params, json_schema) + def max_chars = params_max_chars(params_map) + for (group in params_map.keySet()) { + def group_params = params_map.get(group) // This gets the parameters of that particular group + if (group_params) { + output += group + "\n" + for (param in group_params.keySet()) { + output += " \u001B[1m" + param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + "\n" + } + output += "\n" + } + } + output += Headers.dashed_line(params.monochrome_logs) + output += "\n\n" + Checks.citation(workflow) + output += "\n\n" + Headers.dashed_line(params.monochrome_logs) + return output + } + + static String params_summary_multiqc(workflow, summary) { + String summary_section = '' + for (group in summary.keySet()) { + def group_params = summary.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()) { + summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" + } + summary_section += "
\n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + 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 += "${summary_section}" + return yaml_file_text + } +} diff --git a/main.nf b/main.nf new file mode 100644 index 00000000..a7f7b172 --- /dev/null +++ b/main.nf @@ -0,0 +1,164 @@ +#!/usr/bin/env nextflow +/* +======================================================================================== + nf-core/cutandrun +======================================================================================== + nf-core/cutandrun Analysis Pipeline. + #### Homepage / Documentation + https://github.com/nf-core/cutandrun +---------------------------------------------------------------------------------------- +*/ + +nextflow.enable.dsl = 2 + +//////////////////////////////////////////////////// +/* -- PRINT HELP -- */ +//////////////////////////////////////////////////// + +def json_schema = "$projectDir/nextflow_schema.json" +if (params.help) { + // TODO nf-core: Update typical command used to run pipeline + def command = "nextflow run nf-core/cutandrun --input samplesheet.csv -profile docker" + log.info Schema.params_help(workflow, params, json_schema, command) + exit 0 +} + +//////////////////////////////////////////////////// +/* -- GENOME PARAMETER VALUES -- */ +//////////////////////////////////////////////////// + +params.fasta = Checks.get_genome_attribute(params, 'fasta') + +//////////////////////////////////////////////////// +/* -- PRINT PARAMETER SUMMARY -- */ +//////////////////////////////////////////////////// + +def summary_params = Schema.params_summary_map(workflow, params, json_schema) +log.info Schema.params_summary_log(workflow, params, json_schema) + +//////////////////////////////////////////////////// +/* -- PARAMETER CHECKS -- */ +//////////////////////////////////////////////////// + +// Check that conda channels are set-up correctly +if (params.enable_conda) { + Checks.check_conda_channels(log) +} + +// Check AWS batch settings +Checks.aws_batch(workflow, params) + +// Check the hostnames against configured profiles +Checks.hostname(workflow, params, log) + +// Check genome key exists if provided +Checks.genome_exists(params, log) + +//////////////////////////////////////////////////// +/* -- VALIDATE INPUTS -- */ +//////////////////////////////////////////////////// + +// TODO nf-core: Add all file path parameters for the pipeline to the list below +// Check input path parameters to see if they exist +checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] +for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } + +// Check mandatory parameters +if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +if (params.fasta) { ch_fasta = file(params.fasta) } else { exit 1, 'Genome fasta file not specified!' } + +//////////////////////////////////////////////////// +/* -- CONFIG FILES -- */ +//////////////////////////////////////////////////// + +ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() + +//////////////////////////////////////////////////// +/* -- IMPORT MODULES / SUBWORKFLOWS -- */ +//////////////////////////////////////////////////// + +// Don't overwrite global params.modules, create a copy instead and use that within the main script. +def modules = params.modules.clone() + +def multiqc_options = modules['multiqc'] +multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title\"" : '' + +// Local: Modules +include { GET_SOFTWARE_VERSIONS } from './modules/local/process/get_software_versions' addParams( options: [publish_files : ['csv':'']] ) + +// Local: Sub-workflows +include { INPUT_CHECK } from './modules/local/subworkflow/input_check' addParams( options: [:] ) + +// nf-core/modules: Modules +include { FASTQC } from './modules/nf-core/software/fastqc/main' addParams( options: modules['fastqc'] ) +include { MULTIQC } from './modules/nf-core/software/multiqc/main' addParams( options: multiqc_options ) + +//////////////////////////////////////////////////// +/* -- RUN MAIN WORKFLOW -- */ +//////////////////////////////////////////////////// + +// Info required for completion email and summary +def multiqc_report = [] + +workflow { + + ch_software_versions = Channel.empty() + + /* + * SUBWORKFLOW: Read in samplesheet, validate and stage input files + */ + INPUT_CHECK ( + ch_input + ) + + /* + * MODULE: Run FastQC + */ + FASTQC ( + INPUT_CHECK.out.reads + ) + ch_software_versions = ch_software_versions.mix(FASTQC.out.version.first().ifEmpty(null)) + + + /* + * MODULE: Pipeline reporting + */ + GET_SOFTWARE_VERSIONS ( + ch_software_versions.map { it }.collect() + ) + + /* + * MultiQC + */ + if (!params.skip_multiqc) { + workflow_summary = Schema.params_summary_multiqc(workflow, summary_params) + ch_workflow_summary = Channel.value(workflow_summary) + + ch_multiqc_files = Channel.empty() + ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) + ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(GET_SOFTWARE_VERSIONS.out.yaml.collect()) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + + MULTIQC ( + ch_multiqc_files.collect() + ) + multiqc_report = MULTIQC.out.report.toList() + ch_software_versions = ch_software_versions.mix(MULTIQC.out.version.ifEmpty(null)) + } +} + +//////////////////////////////////////////////////// +/* -- COMPLETION EMAIL -- */ +//////////////////////////////////////////////////// + +workflow.onComplete { + Completion.email(workflow, params, summary_params, projectDir, log, multiqc_report) + Completion.summary(workflow, params, log) +} + +//////////////////////////////////////////////////// +/* -- THE END -- */ +//////////////////////////////////////////////////// diff --git a/modules/local/process/functions.nf b/modules/local/process/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/modules/local/process/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/modules/local/process/get_software_versions.nf b/modules/local/process/get_software_versions.nf new file mode 100644 index 00000000..7ad04057 --- /dev/null +++ b/modules/local/process/get_software_versions.nf @@ -0,0 +1,32 @@ +// Import generic module functions +include { saveFiles } from './functions' + +params.options = [:] + +/* + * Parse software version numbers + */ +process GET_SOFTWARE_VERSIONS { + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', publish_id:'') } + + conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + container "quay.io/biocontainers/python:3.8.3" + + cache false + + input: + path versions + + output: + path "software_versions.csv" , emit: csv + path 'software_versions_mqc.yaml', emit: yaml + + script: + """ + echo $workflow.manifest.version > pipeline.version.txt + echo $workflow.nextflow.version > nextflow.version.txt + scrape_software_versions.py &> software_versions_mqc.yaml + """ +} diff --git a/modules/local/process/samplesheet_check.nf b/modules/local/process/samplesheet_check.nf new file mode 100644 index 00000000..65a80732 --- /dev/null +++ b/modules/local/process/samplesheet_check.nf @@ -0,0 +1,50 @@ +// Import generic module functions +include { saveFiles } from './functions' + +params.options = [:] + +/* + * Reformat design file and check validity + */ +process SAMPLESHEET_CHECK { + tag "$samplesheet" + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', publish_id:'') } + + conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + container "quay.io/biocontainers/python:3.8.3" + + input: + path samplesheet + + output: + path '*.csv' + + + script: // This script is bundled with the pipeline, in nf-core/cutandrun/bin/ + """ + check_samplesheet.py $samplesheet samplesheet.valid.csv + """ +} + +// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] +def get_samplesheet_paths(LinkedHashMap row) { + def meta = [:] + meta.id = row.sample + meta.single_end = row.single_end.toBoolean() + + def array = [] + if (!file(row.fastq_1).exists()) { + exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" + } + if (meta.single_end) { + array = [ meta, [ file(row.fastq_1) ] ] + } else { + if (!file(row.fastq_2).exists()) { + exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" + } + array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] + } + return array +} diff --git a/modules/local/subworkflow/input_check.nf b/modules/local/subworkflow/input_check.nf new file mode 100644 index 00000000..cb6a902d --- /dev/null +++ b/modules/local/subworkflow/input_check.nf @@ -0,0 +1,23 @@ +/* + * Check input samplesheet and get read channels + */ + +params.options = [:] + +include { + SAMPLESHEET_CHECK; + get_samplesheet_paths } from '../process/samplesheet_check' addParams( options: params.options ) + +workflow INPUT_CHECK { + take: + samplesheet // file: /path/to/samplesheet.csv + + main: + SAMPLESHEET_CHECK ( samplesheet ) + .splitCsv ( header:true, sep:',' ) + .map { get_samplesheet_paths(it) } + .set { reads } + + emit: + reads // channel: [ val(meta), [ reads ] ] +} diff --git a/modules/nf-core/software/fastqc/functions.nf b/modules/nf-core/software/fastqc/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/modules/nf-core/software/fastqc/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/modules/nf-core/software/fastqc/main.nf b/modules/nf-core/software/fastqc/main.nf new file mode 100644 index 00000000..3cb510ac --- /dev/null +++ b/modules/nf-core/software/fastqc/main.nf @@ -0,0 +1,47 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process FASTQC { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0" + } else { + container "quay.io/biocontainers/fastqc:0.11.9--0" + } + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip") , emit: zip + path "*.version.txt" , emit: version + + script: + // Add soft-links to original FastQs for consistent naming in pipeline + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" + if (meta.single_end) { + """ + [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz + fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz + fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt + """ + } else { + """ + [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz + [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz + fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz + fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt + """ + } +} diff --git a/modules/nf-core/software/fastqc/meta.yml b/modules/nf-core/software/fastqc/meta.yml new file mode 100644 index 00000000..413aad8d --- /dev/null +++ b/modules/nf-core/software/fastqc/meta.yml @@ -0,0 +1,72 @@ +name: fastqc +description: Run FastQC on sequenced reads +keywords: + - quality control + - qc + - adapters + - fastq +tools: + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +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. +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}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/software/multiqc/functions.nf b/modules/nf-core/software/multiqc/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/modules/nf-core/software/multiqc/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/modules/nf-core/software/multiqc/main.nf b/modules/nf-core/software/multiqc/main.nf new file mode 100644 index 00000000..ff1175fc --- /dev/null +++ b/modules/nf-core/software/multiqc/main.nf @@ -0,0 +1,35 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process MULTIQC { + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') } + + conda (params.enable_conda ? "bioconda::multiqc=1.9" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0" + } else { + container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0" + } + + input: + path multiqc_files + + output: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + """ + multiqc -f $options.args . + multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt + """ +} diff --git a/modules/nf-core/software/multiqc/meta.yml b/modules/nf-core/software/multiqc/meta.yml new file mode 100644 index 00000000..02f4b415 --- /dev/null +++ b/modules/nf-core/software/multiqc/meta.yml @@ -0,0 +1,60 @@ +name: MultiQC +description: Aggregate results from bioinformatics analyses across many samples into a single report +keywords: + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report +tools: + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC +output: + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@abhi18av" + - "@bunop" + - "@drpatelh" diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 00000000..a79f38fc --- /dev/null +++ b/nextflow.config @@ -0,0 +1,164 @@ +/* + * ------------------------------------------------- + * nf-core/cutandrun Nextflow config file + * ------------------------------------------------- + * Default config options for all environments. + */ + +// Global default params, used in configs +params { + + // TODO nf-core: Specify your pipeline's command line flags + // Input options + input = '' + + // References + genome = '' + igenomes_base = 's3://ngi-igenomes/igenomes/' + igenomes_ignore = false + + // MultiQC options + multiqc_config = '' + multiqc_title = '' + max_multiqc_email_size = '25.MB' + skip_multiqc = false + + // Boilerplate options + outdir = './results' + tracedir = "${params.outdir}/pipeline_info" + publish_dir_mode = 'copy' + email = '' + email_on_fail = '' + plaintext_email = false + monochrome_logs = false + help = false + enable_conda = false + singularity_pull_docker_container = false + + // Config options + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + hostnames = [:] + config_profile_description = '' + config_profile_contact = '' + config_profile_url = '' + + // Max resource options + // Defaults only, expecting to be overwritten + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' + +} + +// Load base.config by default for all pipelines +includeConfig 'conf/base.config' + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.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 igenomes.config if required +if (!params.igenomes_ignore) { + includeConfig 'conf/igenomes.config' +} else { + params.genomes = [:] +} + +profiles { + debug { process.beforeScript = 'echo $HOSTNAME' } + conda { params.enable_conda = true } + docker { + docker.enabled = true + // Avoid this error: + // WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. + // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351 + // once this is established and works well, nextflow might implement this behavior as new default. + docker.runOptions = '-u \$(id -u):\$(id -g)' + } + singularity { + singularity.enabled = true + singularity.autoMounts = true + } + podman { + podman.enabled = true + } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } +} + +// Export these variables to prevent local Python/R libraries from conflicting with those in the container +env { + PYTHONNOUSERSITE = 1 + R_PROFILE_USER = "/.Rprofile" + R_ENVIRON_USER = "/.Renviron" +} + +// Capture exit codes from upstream processes when piping +process.shell = ['/bin/bash', '-euo', 'pipefail'] + +timeline { + enabled = true + file = "${params.tracedir}/execution_timeline.html" +} +report { + enabled = true + file = "${params.tracedir}/execution_report.html" +} +trace { + enabled = true + file = "${params.tracedir}/execution_trace.txt" +} +dag { + enabled = true + file = "${params.tracedir}/pipeline_dag.svg" +} + +manifest { + name = 'nf-core/cutandrun' + author = 'Chris Cheshire and Charlotte West' + homePage = 'https://github.com/nf-core/cutandrun' + description = 'Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.' + mainScript = 'main.nf' + nextflowVersion = '!>=20.11.0-edge' + version = '1.0dev' +} + +// Function to ensure that resource requirements don't go beyond +// a maximum limit +def check_max(obj, type) { + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${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: $obj" + return obj + } + } +} diff --git a/nextflow_schema.json b/nextflow_schema.json new file mode 100644 index 00000000..931d89ab --- /dev/null +++ b/nextflow_schema.json @@ -0,0 +1,265 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/cutandrun/master/nextflow_schema.json", + "title": "nf-core/cutandrun pipeline parameters", + "description": "Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": [ + "input" + ], + "properties": { + "input": { + "type": "string", + "description": "Path to comma-separated file containing information about the samples in the experiment.", + "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location.", + "fa_icon": "fas fa-file-csv" + }, + "outdir": { + "type": "string", + "description": "Path to the output directory where the results will be saved.", + "default": "./results", + "fa_icon": "fas fa-folder-open" + }, + "email": { + "type": "string", + "description": "Email address for completion summary.", + "fa_icon": "fas fa-envelope", + "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" + } + } + }, + "reference_genome_options": { + "title": "Reference genome options", + "type": "object", + "fa_icon": "fas fa-dna", + "description": "Reference genome related files and options required for the workflow.", + "properties": { + "genome": { + "type": "string", + "description": "Name of iGenomes reference.", + "fa_icon": "fas fa-book", + "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." + }, + "fasta": { + "type": "string", + "description": "Path to FASTA genome file.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified.", + "fa_icon": "far fa-file-code" + }, + "igenomes_base": { + "type": "string", + "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.", + "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`." + } + } + }, + "institutional_config_options": { + "title": "Institutional config options", + "type": "object", + "fa_icon": "fas fa-university", + "description": "Parameters used to describe centralised config profiles. These should not be edited.", + "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", + "properties": { + "custom_config_version": { + "type": "string", + "description": "Git commit id for Institutional configs.", + "default": "master", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "custom_config_base": { + "type": "string", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", + "hidden": true, + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "fa_icon": "fas fa-users-cog" + }, + "hostnames": { + "type": "string", + "description": "Institutional configs hostname.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_description": { + "type": "string", + "description": "Institutional config description.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_contact": { + "type": "string", + "description": "Institutional config contact information.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_url": { + "type": "string", + "description": "Institutional config URL link.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + } + } + }, + "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", + "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", + "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", + "fa_icon": "fas fa-file-import", + "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 + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], + "hidden": true + }, + "email_on_fail": { + "type": "string", + "description": "Email address for completion summary, only when pipeline fails.", + "fa_icon": "fas fa-exclamation-triangle", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$", + "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.", + "hidden": true + }, + "plaintext_email": { + "type": "boolean", + "description": "Send plain-text email instead of HTML.", + "fa_icon": "fas fa-remove-format", + "hidden": true + }, + "tracedir": { + "type": "string", + "description": "Directory to keep pipeline Nextflow logs and reports.", + "default": "${params.outdir}/pipeline_info", + "fa_icon": "fas fa-cogs", + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Do not use coloured log outputs.", + "fa_icon": "fas fa-palette", + "hidden": true + }, + "skip_multiqc": { + "type": "boolean", + "description": "Skip MultiQC.", + "fa_icon": "fas fa-fast-forward" + }, + "multiqc_config": { + "type": "string", + "description": "Custom config file to supply to MultiQC.", + "fa_icon": "fas fa-cog", + "hidden": true + }, + "multiqc_title": { + "type": "string", + "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", + "fa_icon": "fas fa-file-signature" + }, + "max_multiqc_email_size": { + "type": "string", + "description": "File size limit when attaching MultiQC reports to summary emails.", + "default": "25.MB", + "fa_icon": "fas fa-file-upload", + "hidden": true + }, + "enable_conda": { + "type": "boolean", + "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", + "hidden": true, + "fa_icon": "fas fa-bacon" + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.", + "hidden": true, + "fa_icon": "fas fa-toolbox", + "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues." + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/reference_genome_options" + }, + { + "$ref": "#/definitions/institutional_config_options" + }, + { + "$ref": "#/definitions/max_job_request_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} \ No newline at end of file