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Merge pull request #5 from maxulysse/dev
FEAT: add CNVKIT + base skeleton
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,194 @@ | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| name: nf-core CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| pull_request: | ||
| branches: | ||
| - dev | ||
| - master | ||
| release: | ||
| types: [published] | ||
| types: | ||
| - "published" | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.7.3" | ||
|
|
||
| # Cancel if a newer run is started | ||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| test: | ||
| name: Run pipeline with test data | ||
| # 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/createpanelrefs') }}" | ||
| changes: | ||
| name: Check for changes | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| # Expose matched filters as job 'tags' output variable | ||
| tags: ${{ steps.filter.outputs.changes }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: dorny/paths-filter@v2 | ||
| id: filter | ||
| with: | ||
| filters: "tests/config/tags.yml" | ||
|
|
||
| define_nxf_versions: | ||
| name: Choose nextflow versions to test against depending on target branch | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.nxf_versions.outputs.matrix }} | ||
| steps: | ||
| - id: nxf_versions | ||
| run: | | ||
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | ||
| echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT | ||
| else | ||
| echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT | ||
| fi | ||
| test-dev: | ||
| if: (github.base_ref == 'dev' || (github.event_name == 'push')) | ||
| name: ${{ matrix.tags }} ${{ matrix.profile }} NXF ${{ matrix.NXF_VER }} | ||
| runs-on: ubuntu-latest | ||
| needs: changes | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| # Run tests based on changes in code | ||
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | ||
| # Only run docker tests on dev branch | ||
| profile: ["docker"] | ||
| # Only test minimal version | ||
| NXF_VER: ["23.04.0"] | ||
| # Always run default test | ||
| include: | ||
| - tags: default | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| - name: Install nf-test | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: Install Nextflow ${{ matrix.NXF_VER }} | ||
| uses: nf-core/[email protected] | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - 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 | ||
| - name: Run nf-test | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nf-test test tests/pipeline/${{ matrix.tags }}.nf.test --profile "test,${{ matrix.profile }}" --tap=test.tap | ||
| attempt_limit: 3 | ||
|
|
||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | ||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: logs-${{ matrix.profile }} | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/work | ||
| test-master: | ||
| # Only run on master branch or when a PR is opened against master | ||
| if: github.base_ref == 'master' | ||
| name: ${{ matrix.tags }} ${{ matrix.profile }} NXF ${{ matrix.NXF_VER }} | ||
| runs-on: ubuntu-latest | ||
| needs: [changes, define_nxf_versions] | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| # Run tests based on changes in code | ||
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | ||
| # Only run docker tests on dev branch | ||
| profile: ["docker", "singularity", "conda"] | ||
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | ||
| # Always run default test | ||
| include: | ||
| - tags: default | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| - name: Install nf-test | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: Install Nextflow ${{ matrix.NXF_VER }} | ||
| uses: nf-core/[email protected] | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
|
|
||
| - name: Set up miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| channels: conda-forge,bioconda,defaults | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| - name: Conda clean | ||
| if: matrix.profile == 'conda' | ||
| run: conda clean -a | ||
|
|
||
| - name: Run nf-test | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nf-test test tests/pipeline/${{ matrix.tag }}.nf.test --profile "test,${{ matrix.profile }}" --tap=test.tap | ||
| attempt_limit: 3 | ||
|
|
||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | ||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: logs-${{ matrix.profile }} | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/work | ||
| !/home/runner/pytest_workflow_*/*/work/conda | ||
| !/home/runner/pytest_workflow_*/*/work/singularity |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,9 @@ | ||
| *.pyc | ||
| .DS_Store | ||
| .nextflow* | ||
| work/ | ||
| .nf-test/ | ||
| data/ | ||
| results/ | ||
| .DS_Store | ||
| testing/ | ||
| testing* | ||
| *.pyc | ||
| testing/ | ||
| work/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,8 @@ | ||
| repository_type: pipeline | ||
| lint: | ||
| actions_ci: False | ||
| files_exist: | ||
| - conf/modules.config | ||
| files_unchanged: | ||
| - .gitattributes | ||
| - .gitignore |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,13 @@ | ||
| email_template.html | ||
| adaptivecard.json | ||
| slackreport.json | ||
| *.pyc | ||
| .DS_Store | ||
| .nextflow* | ||
| work/ | ||
| .nf-test/ | ||
| adaptivecard.json | ||
| bin/ | ||
| data/ | ||
| email_template.html | ||
| results/ | ||
| .DS_Store | ||
| testing/ | ||
| slackreport.json | ||
| testing* | ||
| *.pyc | ||
| bin/ | ||
| testing/ | ||
| work/ |
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