V1.8.5 #63
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| # This is a basic workflow to help you get started with Actions | |
| name: gsalign | |
| # Controls when the action will run. | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| - 'dev' | |
| - 'dev/' | |
| - '*CI' | |
| - 'v*' | |
| pull_request: | |
| workflow_dispatch: | |
| release: | |
| types: [published] | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| test: | |
| name: Run workflow tests | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name == 'push' }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| nxf_ver: ["24.04.4"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Install mamba | |
| run: | | |
| wget -nv -O Mambaforge.sh /~https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh | |
| bash Mambaforge.sh -b -p ./mambaforge | |
| ./mambaforge/bin/mamba init | |
| source ./mambaforge/etc/profile.d/conda.sh | |
| - name: Run pipeline with test data and GSAlign | |
| run: | | |
| source ./mambaforge/etc/profile.d/conda.sh | |
| nextflow run ${GITHUB_WORKSPACE} --aligner gsalign --mamba -profile test,conda |