fix DADA issues; this should still be tested further but works for now #96
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 | |
| 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 | |