Use original QC values for Deepvariant after BQSR #6536
Workflow file for this run
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| 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] | |
| workflow_dispatch: | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| NFT_VER: "0.9.0" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| filter: ["workflow", "function", "pipeline"] | |
| # filter: ["process", "workflow", "function", "pipeline"] | |
| profile: ["conda", "docker", "singularity"] | |
| shard: [1, 2, 3, 4, 5] | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - 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 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: Set up nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_VER }} | |
| - name: Set up 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: Cache pdiff | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| id: cache-pip-pdiff | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-pdiff | |
| - name: Install pdiff | |
| run: python -m pip install --upgrade pip pdiff cryptography | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Disk space cleanup | |
| uses: jlumbroso/[email protected] | |
| - name: Start summary | |
| id: print-test | |
| run: | | |
| echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "This \`${{ matrix.filter }}\` ${{ matrix.shard }}/5 shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| nf-test test \ | |
| --ci \ | |
| --dryRun \ | |
| --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | |
| --shard ${{ matrix.shard }}/5 \ | |
| --changed-since HEAD^ \ | |
| --follow-dependencies \ | |
| --profile "+${{ matrix.profile }}" \ | |
| --filter ${{ matrix.filter }} \ | |
| | grep PASSED | cut -d "'" -f 2 | sed 's/^/- /' | sort -u >> $GITHUB_STEP_SUMMARY | |
| - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5" | |
| run: | | |
| nf-test test \ | |
| --ci \ | |
| --debug \ | |
| --verbose \ | |
| --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | |
| --shard ${{ matrix.shard }}/5 \ | |
| --changed-since HEAD^ \ | |
| --follow-dependencies \ | |
| --profile "+${{ matrix.profile }}" \ | |
| --filter ${{ matrix.filter }} | |
| - name: Print success in summary | |
| if: success() | |
| run: | | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "All test(s) successfull :tada:" >> $GITHUB_STEP_SUMMARY | |
| - name: Print failure in summary | |
| if: failure() | |
| run: | | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "Some test(s) failed :cold_sweat:" >> $GITHUB_STEP_SUMMARY | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v4 | |
| if: success() || failure() # always run even if the previous step fails | |
| with: | |
| report_paths: "TEST-*.xml" | |
| - name: Clean up | |
| if: success() || failure() | |
| run: | | |
| sudo rm -rf /home/ubuntu/tests/ |