Update modules #1008
Workflow file for this run
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| name: pytest-workflow | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| pull_request: | |
| branches: [dev] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| 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" | |
| test: | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
| runs-on: ubuntu-latest | |
| needs: changes | |
| if: needs.changes.outputs.tags != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | |
| profile: ["docker"] | |
| # profile: ["docker", "singularity", "conda"] | |
| TEST_DATA_BASE: | |
| - "test-datasets/data" | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| exclude: | |
| # - profile: "conda" | |
| # tags: concatenate_vcfs | |
| # - profile: "conda" | |
| # tags: deepvariant | |
| # - profile: "conda" | |
| # tags: haplotypecaller | |
| # - profile: "conda" | |
| # tags: merge | |
| # - profile: "conda" | |
| # tags: snpeff | |
| # - profile: "conda" | |
| # tags: umi | |
| # - profile: "conda" | |
| # tags: validation_checks | |
| # - profile: "conda" | |
| # tags: vep | |
| # - profile: "conda" | |
| # tags: sentieon/bwamem | |
| - profile: "singularity" | |
| tags: concatenate_vcfs | |
| - profile: "singularity" | |
| tags: merge | |
| - profile: "singularity" | |
| tags: validation_checks | |
| env: | |
| NXF_ANSI_LOG: false | |
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: sarek3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in tests/csv/3.0/*csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| 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 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow ${{ matrix.NXF_VER }} | |
| uses: nf-core/setup-nextflow@v1.2.0 | |
| with: | |
| version: "${{ 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 }} | |
| # 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 bin/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 $SENTIEON_AUTH_DATA_BASE64 | |
| - name: Conda clean | |
| if: matrix.profile == 'conda' | |
| run: conda clean -a | |
| - name: Run pytest-workflow | |
| uses: Wandalen/wretry.action@v1.0.11 | |
| with: | |
| command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
| attempt_limit: 3 | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-${{ 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 |