dhatribadri is testing snakemake workflow 🚀 #42
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| name: Test QCD Pipeline | |
| run-name: ${{ github.actor }} is testing snakemake workflow 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Test-QCD-Pipeline: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event." | |
| # - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!" | |
| # - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}." | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner." | |
| - run: echo "🖥️ The workflow is now ready to test your code on the runner." | |
| - name: Set up sysctl for unprivileged user namespaces | |
| run: | | |
| sudo sh -c 'echo kernel.unprivileged_userns_clone=1 > /etc/sysctl.d/90-unprivileged_userns.conf' | |
| sudo sysctl -p /etc/sysctl.d/90-unprivileged_userns.conf | |
| # Set up Dropbox CLI | |
| # - name: Set up Dropbox CLI | |
| # # run: | | |
| # # curl -L https://www.dropbox.com/download?dl=packages/ubuntu/dropbox_2020.03.04_amd64.deb -o dropbox.deb | |
| # # sudo dpkg -i dropbox.deb | |
| # # sudo apt-get install -f | |
| # # - name: Install Dropbox CLI | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install -y \ | |
| # libpango1.0-0 \ | |
| # gir1.2-gtk-3.0 \ | |
| # gir1.2-pango-1.0 | |
| # curl -L https://www.dropbox.com/download?dl=packages/ubuntu/dropbox_2020.03.04_amd64.deb -o dropbox.deb | |
| # sudo dpkg -i dropbox.deb | |
| # sudo apt-get install -f -y | |
| # - name: Locate Dropbox CLI | |
| # run: | | |
| # sudo find / -name "dropbox-cli" || echo "Dropbox CLI not found" | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # - name: Authenticate with Dropbox | |
| # run: | | |
| # export DROPBOX_TOKEN=${{ secrets.DROPBOX_TOKEN }} | |
| # dropbox start -i | |
| # dropbox login $DROPBOX_TOKEN | |
| - name: List files in the repository | |
| run: | | |
| ls | |
| - name: Get working directory | |
| run: | | |
| pwd | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: '3.10' | |
| auto-update-conda: true | |
| activate-environment: 'qcd_env_test' | |
| environment-file: 'qcd_environment.yaml' | |
| use-channel-priority: true | |
| - name: Install singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Install pip dependencies | |
| run: | | |
| source $CONDA/bin/activate | |
| conda activate qcd_env_test | |
| pip install --requirement .test/requirements.txt | |
| pip install dropbox | |
| pip install --upgrade tabulate | |
| pip install --upgrade snakemake | |
| # # Debugging step: Print environment variables | |
| # - name: Print environment variables | |
| # run: printenv | |
| # Download FASTQ files from Dropbox | |
| - name: Download FASTQ files from Dropbox and copy it to local path | |
| env: | |
| DROPBOX_ACCESS_TOKEN: ${{ secrets.DROPBOX_ACCESS_TOKEN }} | |
| run: | | |
| source $CONDA/bin/activate | |
| conda activate qcd_env_test | |
| export DROPBOX_ACCESS_TOKEN=${DROPBOX_ACCESS_TOKEN} | |
| python3 download_fastqs.py | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Create necessary directories | |
| run: | | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/quality_raw | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/trimmomatic | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/raw_coverage | |
| - name: Snakemake workflow | |
| # run: | | |
| # snakemake -s QCD.smk -p --use-conda --use-singularity -j 999 --conda-frontend conda --cluster-config config/cluster.json --configfile config/config.yaml --latency-wait 1000 --cores 4 | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: '.' | |
| snakefile: 'QCD.smk' | |
| args: '--cores 4 --use-conda --use-singularity --use-envmodules --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000' | |
| #run: echo "🍏 This job's status is ${{ job.status }}." |