Dev2rc #438
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hicar') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| parameters: | |
| - "--interactions_tool maps" | |
| - "--interactions_tool hicdcplus" | |
| - "--interactions_tool peakachu" | |
| - "--tad_tool homer" | |
| - "--compartments_tool homer" | |
| - "--compartments_tool juicebox" | |
| - "--do_apa --apa_tool juicebox" | |
| - "--do_apa --apa_tool cooltools" | |
| - "--da_tool edger" | |
| - "--da_tool setOperation" | |
| - "--da_tool hicexplorer" | |
| - "--v4c_tool cooltools --v4c_max_events 3" | |
| - "--v4c_tool trackviewer --v4c_max_events 3" | |
| - "--method HiChIP --anchor_peaks 'https://raw.githubusercontent.com/aryeelab/hichipper/master/tests/chipseq/GM12878_SMC3_ChIPSeq_chr22.narrowPeak'" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} | |
| # |