updating BioNF #8
Workflow file for this run
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| name: mop3-CI | |
| # When this workflow is triggered | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'docs/**' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| jobs: | |
| build: | |
| name: mop3 ci | |
| # This job runs on Linux | |
| runs-on: ubuntu-20.04 | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [11] | |
| steps: | |
| - name: Delete huge unnecessary tools folder | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: true | |
| - name: Environment | |
| run: env | sort | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| token: ${{ github.token }} | |
| repository: biocorecrg/master_of_pores | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup Java | |
| uses: actions/setup-java@v2 | |
| with: | |
| java-version: ${{ matrix.java_version }} | |
| distribution: 'adopt' | |
| architecture: x64 | |
| - name: MOP3 | |
| run: | | |
| curl -fsSL get.nextflow.io | bash | |
| bash INSTALL.sh | |
| cd mop_preprocess | |
| ../nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-docker -profile ci | |
| cd ../mop_mod | |
| ../nextflow run mop_mod.nf -params-file params.yaml -with-docker -profile ci | |
| cd ../mop_tail | |
| ../nextflow run mop_tail.nf -with-docker -params-file params.yaml -profile ci | |
| env: | |
| NXF_ANSI_LOG: false |