update workflow singularity #9
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| name: Nextflow CI | |
| on: | |
| push: | |
| branches: | |
| - development | |
| jobs: | |
| test_sarscov2_user: | |
| name: Run pipeline test (user) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Install Singularity | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| wget \ | |
| pkg-config \ | |
| git \ | |
| cryptsetup | |
| wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb | |
| sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb | |
| - name: Run pipeline test (user) | |
| run: | | |
| nextflow run main.nf -profile singularity --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml | |
| test_sarscov2_reference: | |
| name: Run pipeline test (reference) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Install Singularity | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| wget \ | |
| pkg-config \ | |
| git \ | |
| cryptsetup | |
| wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb | |
| sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb | |
| - name: Run pipeline test (reference) | |
| run: | | |
| nextflow run main.nf -profile singularity --prefix "covidmvp-$(date +%Y-%m-%d)" -params-file covidmvp_clinical_params.yaml |