Install Singularity in act-nextflow Docker container #14
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: CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that | |
| # it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - 260-improve-ci | |
| 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 in the main repository | |
| if: "${{ github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/jasen' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.10.1" | |
| parameters: | |
| - "-profile staphylococcus_aureus" | |
| #- "-profile mycobacterium_tuberculosis" | |
| #- "-profile klebsiella_pneumoniae" | |
| #- "-profile escherichia_coli" | |
| steps: | |
| - name: Install Nextflow | |
| # For running (locally) with ACT, we use a docker image with Nextflow pre-installed | |
| if: "${{ ! github.event.act }}" | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE}/main.nf ${{ matrix.parameters }} -config configs/nextflow.ci.config --csv assets/test_data/samplelist.testrun.csv |