Add output containing per-tool quantification #1145
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] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/circrna') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - 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 | |
| run: | | |
| echo "digest=$(echo RNA_3.10.1_${{ 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: circrna | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in ${{ github.workspace }}/test-datasets/*.csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/circrna/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets |