Add INITIALISE subworkflow for starting nf-core pipelines (#3847) #47
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| name: test | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| jobs: | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@v3 | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-node@v3 | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
| pytest-changes: | |
| name: pytest-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| nf-core-lint: | |
| runs-on: ubuntu-20.04 | |
| name: nf-core-lint | |
| needs: [pytest-changes] | |
| if: needs.pytest-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] | |
| exclude: | |
| - tags: "nf-test" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Lint ${{ matrix.tags }} | |
| run: nf-core modules lint ${{ matrix.tags }} | |
| # HACK | |
| if: startsWith( matrix.tags, 'subworkflow' ) != true | |
| pytest: | |
| runs-on: ubuntu-20.04 | |
| name: pytest | |
| needs: [pytest-changes] | |
| if: needs.pytest-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: annotsv | |
| - profile: "conda" | |
| tags: cellpose | |
| - profile: "conda" | |
| tags: mcquant | |
| - profile: "conda" | |
| tags: bases2fastq | |
| - profile: "conda" | |
| tags: backsub | |
| - profile: "conda" | |
| tags: basicpy | |
| - profile: "conda" | |
| tags: bcl2fastq | |
| - profile: "conda" | |
| tags: bclconvert | |
| - profile: "conda" | |
| tags: cellranger/count | |
| - profile: "conda" | |
| tags: cellranger/mkfastq | |
| - profile: "conda" | |
| tags: cellranger/mkgtf | |
| - profile: "conda" | |
| tags: cellranger/mkref | |
| - profile: "conda" | |
| tags: cellranger/mkvdjref | |
| - profile: "conda" | |
| tags: cellranger/multi | |
| - profile: "conda" | |
| tags: cellranger/vdj | |
| - profile: "conda" | |
| tags: coreograph | |
| - profile: "conda" | |
| tags: deepcell/mesmer | |
| - profile: "conda" | |
| tags: deepvariant | |
| - profile: "conda" | |
| tags: fastk/fastk | |
| - profile: "conda" | |
| tags: fastk/histex | |
| - profile: "conda" | |
| tags: fastk/merge | |
| - profile: "conda" | |
| tags: fcs/fcsadaptor | |
| - profile: "conda" | |
| tags: fcs/fcsgx | |
| - profile: "conda" | |
| tags: gatk4/baserecalibratorspark | |
| - profile: "conda" | |
| tags: gatk4/cnnscorevariants | |
| - profile: "conda" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: gatk4/germlinecnvcaller | |
| - profile: "conda" | |
| tags: gatk4/markduplicatesspark | |
| - profile: "conda" | |
| tags: gatk4/postprocessgermlinecnvcalls | |
| - profile: "conda" | |
| tags: genescopefk | |
| - profile: "conda" | |
| tags: hlala/preparegraph | |
| - profile: "conda" | |
| tags: ilastik/multicut | |
| - profile: "conda" | |
| tags: ilastik/pixelclassification | |
| - profile: "conda" | |
| tags: imputeme/vcftoprs | |
| - profile: "conda" | |
| tags: merquryfk/katcomp | |
| - profile: "conda" | |
| tags: merquryfk/katgc | |
| - profile: "conda" | |
| tags: merquryfk/merquryfk | |
| - profile: "conda" | |
| tags: merquryfk/ploidyplot | |
| - profile: "conda" | |
| tags: mitohifi/mitohifi | |
| - profile: "conda" | |
| tags: mitohifi/findmitoreference | |
| - profile: "conda" | |
| tags: parabricks/applybqsr | |
| - profile: "conda" | |
| tags: parabricks/fq2bam | |
| - profile: "conda" | |
| tags: scimap/mcmicro | |
| - profile: "conda" | |
| tags: sentieon/applyvarcal | |
| - profile: "conda" | |
| tags: sentieon/bwaindex | |
| - profile: "conda" | |
| tags: sentieon/bwamem | |
| - profile: "conda" | |
| tags: sentieon/datametrics | |
| - profile: "conda" | |
| tags: sentieon/dedup | |
| - profile: "conda" | |
| tags: sentieon/dnamodelapply | |
| - profile: "conda" | |
| tags: sentieon/dnascope | |
| - profile: "conda" | |
| tags: sentieon/gvcftyper | |
| - profile: "conda" | |
| tags: sentieon/haplotyper | |
| - profile: "conda" | |
| tags: sentieon/readwriter | |
| - profile: "conda" | |
| tags: sentieon/tnscope | |
| - profile: "conda" | |
| tags: sentieon/varcal | |
| - profile: "conda" | |
| tags: sentieon/wgsmetrics | |
| - profile: "conda" | |
| tags: spaceranger/count | |
| - profile: "conda" | |
| tags: spaceranger/mkgtf | |
| - profile: "conda" | |
| tags: spaceranger/mkref | |
| - profile: "conda" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: subworkflows/bcl_demultiplex | |
| - profile: "conda" | |
| tags: subworkflows/fasta_clean_fcs | |
| - profile: "conda" | |
| tags: islandpath | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow cryptography | |
| - name: Setup Nextflow ${{ matrix.NXF_VER }} | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - 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 setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run pytest-workflow | |
| # only use one thread for pytest-workflow to avoid race condition on conda cache. | |
| run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt-get update > /dev/null | |
| sudo apt-get install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Setting global variables | |
| uses: actions/github-script@v6 | |
| id: parsed | |
| with: | |
| script: | | |
| return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') | |
| result-encoding: string | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} | |
| 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 | |
| !${{ github.workspace }}/.singularity | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: "tests/config/nftest_modules.yml" | |
| nf-test: | |
| runs-on: ubuntu-20.04 | |
| name: nf-test | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: annotsv | |
| - profile: "conda" | |
| tags: bases2fastq | |
| - profile: "conda" | |
| tags: bcl2fastq | |
| - profile: "conda" | |
| tags: bclconvert | |
| - profile: "conda" | |
| tags: cellranger/count | |
| - profile: "conda" | |
| tags: cellranger/mkfastq | |
| - profile: "conda" | |
| tags: cellranger/mkgtf | |
| - profile: "conda" | |
| tags: cellranger/mkref | |
| - profile: "conda" | |
| tags: deepvariant | |
| - profile: "conda" | |
| tags: ensemblvep/vep | |
| - profile: "conda" | |
| tags: fastk/fastk | |
| - profile: "conda" | |
| tags: fastk/histex | |
| - profile: "conda" | |
| tags: fastk/merge | |
| - profile: "conda" | |
| tags: fcs/fcsadaptor | |
| - profile: "conda" | |
| tags: fcs/fcsgx | |
| - profile: "conda" | |
| tags: gatk4/cnnscorevariants | |
| - profile: "conda" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: genescopefk | |
| - profile: "conda" | |
| tags: ilastik/multicut | |
| - profile: "conda" | |
| tags: ilastik/pixelclassification | |
| - profile: "conda" | |
| tags: imputeme/vcftoprs | |
| - profile: "conda" | |
| tags: merquryfk/katcomp | |
| - profile: "conda" | |
| tags: merquryfk/katgc | |
| - profile: "conda" | |
| tags: merquryfk/merquryfk | |
| - profile: "conda" | |
| tags: merquryfk/ploidyplot | |
| - profile: "conda" | |
| tags: sentieon/bwaindex | |
| - profile: "conda" | |
| tags: sentieon/bwamem | |
| - profile: "conda" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: universc | |
| - profile: "conda" | |
| tags: subworkflows/vcf_annotate_ensemblvep | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-nftest | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - 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 setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run nf-test | |
| run: | | |
| nf-test test \ | |
| --profile=${{ matrix.profile }} \ | |
| --tag ${{ matrix.tags }} \ | |
| --tap=test.tap | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |