diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 83dd8f05..4c3df126 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,16 +33,16 @@ jobs: #- "-profile klebsiella_pneumoniae" #- "-profile escherichia_coli" steps: - - name: Check out pipeline code + - name: Install Nextflow # For running (locally) with ACT, we use a docker image with Nextflow pre-installed if: "${{ ! github.event.act }}" - uses: actions/checkout@v3 - - - name: Install Nextflow uses: nf-core/setup-nextflow@v1 with: version: "${{ 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