Get Kinnex-specific pipeline running (experimental) #97
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - master | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| test-illumina: | |
| name: Run workflow tests (Illumina V4) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'h3abionet/TADA') }} | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 45 | |
| permissions: | |
| contents: read | |
| packages: write | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| nxf_ver: ["21.04.0", ""] | |
| profile: | |
| [ | |
| test_illumina, | |
| test_pacbio, | |
| ] | |
| steps: | |
| - name: Checkout pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Set up JDK 11 | |
| uses: actions/setup-java@v2 | |
| with: | |
| java-version: '11' | |
| distribution: 'adopt' | |
| - name: Setup ref-data and test-data directories | |
| run: | | |
| mkdir -p $HOME/ref-data $HOME/test-data/illumina $HOME/test-data/pacbio | |
| cd $HOME/ref-data | |
| wget -nv --no-check-certificate https://file-server.igb.illinois.edu/~cjfields/silva_nr99_v138.1_train_set.fa.gz | |
| wget -nv --no-check-certificate https://file-server.igb.illinois.edu/~cjfields/silva_nr99_v138.1_wSpecies_train_set.fa.gz | |
| cd $HOME/test-data/illumina | |
| wget -nv --no-check-certificate https://file-server.igb.illinois.edu/~cjfields/dog_stool_small.tgz | |
| tar -xzvf dog_stool_small.tgz | |
| cd $HOME/test-data/pacbio | |
| wget -nv --no-check-certificate https://file-server.igb.illinois.edu/~cjfields/Small_PacBio.tgz | |
| tar -xzvf Small_PacBio.tgz | |
| - name: Set up and install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run Nextflow on test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker | |