updating traceback subworkflow with local changes made to pass nf-cor… #684
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| name: Run tests | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main, develop] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [main] | |
| # 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 | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v3 | |
| - uses: pre-commit/action@v3.0.0 | |
| # FIXME Flip this off once we get to less than a couple hundred. Adding | |
| # this so it will only run against changed files. It'll make it much | |
| # easier to fix these as they come up rather than everything at once. | |
| with: | |
| extra_args: "" | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - 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@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| 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@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - name: Combine all tags.yml files | |
| id: get_tags | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| token: "" | |
| nf-core-lint: | |
| runs-on: ubuntu-latest | |
| name: nf-core-lint | |
| needs: [pytest-changes, nf-test-changes] | |
| if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: | |
| [ | |
| "${{ fromJson(needs.pytest-changes.outputs.modules) }}", | |
| "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | |
| ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - 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: Lint module ${{ matrix.tags }} | |
| run: nf-core modules lint ${{ matrix.tags }} | |
| if: ${{ !startsWith(matrix.tags, 'subworkflows/') }} | |
| - name: Remove substring from matrix.tags | |
| id: remove_substring | |
| run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT | |
| - name: Lint subworkflow ${{ matrix.tags }} | |
| run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}} | |
| if: ${{ startsWith(matrix.tags, 'subworkflows/') }} | |
| verify-markdown-file: | |
| runs-on: ubuntu-latest | |
| name: verify-markdown-file | |
| if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} | |
| needs: [pytest-changes, nf-test-changes] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: | |
| [ | |
| "${{ fromJson(needs.pytest-changes.outputs.modules) }}", | |
| "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | |
| ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - name: setup python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Download convertor from yml to md | |
| run: | | |
| curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/yaml_to_md.py | |
| curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/requirements.txt | |
| - name: Give convertor permissions | |
| run: chmod +x yaml_to_md.py | |
| - name: Install python packages | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r ${{ github.workspace }}/requirements.txt | |
| - name: Update ${{ matrix.tags }} | |
| run: | | |
| MATRIX_FRAGMENT="${{ matrix.tags }}" | |
| TEMP_NAME=$(echo $MATRIX_FRAGMENT | sed 's/subworkflows\///g') | |
| SW_NAME=$(echo $TEMP_NAME | sed 's/modules\///g') | |
| echo "SW_NAME=$SW_NAME" >> $GITHUB_ENV | |
| echo $SW_NAME | |
| - uses: jaywcjlove/github-action-read-file@main | |
| id: cat_file_module | |
| with: | |
| branch: ${{ github.ref }} | |
| path: modules/msk/${{ env.SW_NAME }}/meta.yml | |
| - run: echo "${{ steps.cat_file_module.outputs.size }}" | |
| - name: Write Module yaml to temp | |
| if: ${{ steps.cat_file_module.outputs.size }} | |
| id: write_yml_module | |
| run: | | |
| echo '${{ steps.cat_file_module.outputs.content }}' > ${{ github.workspace }}/temp.yml | |
| FEATURE_TYPE="modules" | |
| echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV | |
| - uses: jaywcjlove/github-action-read-file@main | |
| if: ${{ steps.cat_file_module.outputs.size == '' }} | |
| id: cat_file_subworkflow | |
| with: | |
| branch: ${{ github.ref }} | |
| path: subworkflows/msk/${{ env.SW_NAME }}/meta.yml | |
| - name: Write Subworkflow yaml to temp | |
| if: ${{ steps.cat_file_subworkflow.outputs.size }} | |
| id: write_yml_subworkflow | |
| run: | | |
| echo '${{ steps.cat_file_subworkflow.outputs.content }}' > ${{ github.workspace }}/temp.yml | |
| FEATURE_TYPE="subworkflows" | |
| echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV | |
| - name: Run convertor to verify yaml file | |
| run: | | |
| echo ${{ matrix.tags }} | |
| echo ${{ env.FEATURE_TYPE }} | |
| python ${{ github.workspace }}/yaml_to_md.py validate --yaml-file ${{ github.workspace }}/temp.yml --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json | |
| pytest: | |
| runs-on: ubuntu-latest | |
| 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" | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow cryptography | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow ${{ matrix.NXF_VER }} | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Setup apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| # 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 "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python3 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@v3 | |
| 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 | |
| !${{ github.workspace }}/.singularity | |
| nf-test: | |
| runs-on: ubuntu-latest | |
| name: nf-test | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: gbcms | |
| - profile: "conda" | |
| tags: polysolver | |
| - profile: "conda" | |
| tags: snppileup | |
| - profile: "conda" | |
| tags: facets | |
| - profile: "conda" | |
| tags: mutect1 | |
| - profile: "conda" | |
| tags: phylowgs/createinput | |
| - profile: "conda" | |
| tags: phylowgs/parsecnvs | |
| - profile: "conda" | |
| tags: phylowgs/multievolve | |
| - profile: "conda" | |
| tags: phylowgs/writeresults | |
| - profile: "conda" | |
| tags: netmhcpan | |
| - profile: "conda" | |
| tags: neoantigeninput | |
| - profile: "conda" | |
| tags: neoantigenediting/aligntoIEDB | |
| - profile: "conda" | |
| tags: neoantigenediting/computeFitness | |
| - profile: "conda" | |
| tags: subworkflows/neoantigen_editing | |
| - profile: "conda" | |
| tags: subworkflows/phylowgs | |
| - profile: "conda" | |
| tags: netmhcstabpan | |
| - profile: "conda" | |
| tags: ppflagfixer | |
| - profile: "conda" | |
| tags: neoantigenutils/generatemutfasta | |
| - profile: "conda" | |
| tags: neoantigenutils/formatnetmhcpan | |
| - profile: "conda" | |
| tags: neoantigenutils/generatehlastring | |
| - profile: "conda" | |
| tags: neoantigenutils/neoantigeninput | |
| - profile: "conda" | |
| tags: subworkflows/netmhcstabandpan | |
| - profile: "conda" | |
| tags: salmon/index | |
| - profile: "conda" | |
| tags: genomenexus/vcf2maf | |
| - profile: "conda" | |
| tags: genomenexus/annotationpipeline | |
| - profile: "conda" | |
| tags: ppflagfixer | |
| - profile: "conda" | |
| tags: pvmaf/tagtraceback | |
| - profile: "conda" | |
| tags: pvmaf/concat | |
| - profile: "conda" | |
| tags: genotypevariants/all | |
| - profile: "conda" | |
| tags: subworkflows/traceback | |
| - profile: "conda" | |
| tags: salmon/index | |
| - profile: "conda" | |
| tags: subworkflows/genome_nexus | |
| - profile: "conda" | |
| tags: salmon/quant | |
| - profile: "conda" | |
| tags: rediscoverte | |
| - profile: "conda" | |
| tags: neosv | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| NFTEST_VER: "0.8.2" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - 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: ${{ runner.os }}-${{ env.NFTEST_VER }}-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: Setup apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| # 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 "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python3 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 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run nf-test | |
| run: | | |
| NXF_TEST_DIR=~ \ | |
| nf-test test \ | |
| --profile=${{ matrix.profile }} \ | |
| --tag ${{ matrix.tags }} \ | |
| --tap=test.tap \ | |
| --verbose | |
| - 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) }}" |