Process Samples Aspera #1122
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| name: Process Samples Aspera | |
| on: | |
| schedule: | |
| - cron: '0 0-16 * * 0,6' | |
| env: | |
| BATCH_SIZE: 100 | |
| jobs: | |
| setup: | |
| permissions: | |
| contents: write | |
| id-token: write | |
| runs-on: self-hosted | |
| outputs: | |
| run_rest_jobs: ${{ steps.get_accession_list.outputs.run_jobs }} | |
| steps: | |
| - name: Checkout main | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Setup Python | |
| run: | | |
| echo ${{secrets.DPILZ_USR_PWD}} | sudo -S dnf install python3 -y | |
| echo ${{secrets.DPILZ_USR_PWD}} | sudo -S dnf install python3-pip -y | |
| pip3 install pandas numpy pyyaml ffq epiweeks git+https://github.com/outbreak-info/python-outbreak-info.git@new_docs | |
| - name: 'Get accession list' | |
| id: get_accession_list | |
| run: | | |
| python scripts/get_accession_list.py $BATCH_SIZE | |
| if [[ -f data/accession_list.csv ]]; then | |
| echo "::set-output name=run_jobs::true" | |
| else | |
| echo "::set-output name=run_jobs::false" | |
| fi | |
| run_samples: | |
| needs: [setup] | |
| if: needs.setup.outputs.run_rest_jobs == 'true' | |
| permissions: | |
| contents: write | |
| id-token: write | |
| runs-on: self-hosted | |
| steps: | |
| - name: Checkout main | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Setup nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Setup Python | |
| run: | | |
| echo ${{secrets.DPILZ_USR_PWD}} | sudo -S dnf install python3 -y | |
| echo ${{secrets.DPILZ_USR_PWD}} | sudo -S dnf install python3-pip -y | |
| pip3 install pandas numpy pyyaml ffq epiweeks git+https://github.com/outbreak-info/python-outbreak-info.git@new_docs | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v2' | |
| with: | |
| version: '>= 363.0.0' | |
| - id: 'auth' | |
| name: 'Authenticate with gcloud' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| workload_identity_provider: 'projects/12767718289/locations/global/workloadIdentityPools/github/providers/freyja-sra' | |
| service_account: '[email protected]' | |
| - name: 'Get accession list' | |
| id: get_accession_list | |
| run: | | |
| python scripts/get_accession_list.py $BATCH_SIZE | |
| - name: Run pipeline on new samples | |
| run: | | |
| export NXF_ENABLE_VIRTUAL_THREADS=false | |
| nextflow run main.nf \ | |
| --accession_list data/accession_list.csv \ | |
| --num_samples $BATCH_SIZE \ | |
| -profile docker \ | |
| -entry aspera & | |
| BG_PID=$! | |
| wait $BG_PID | |
| - name: Aggregate outputs | |
| run: | | |
| python scripts/aggregate_demix.py | |
| python scripts/aggregate_variants.py | |
| python scripts/aggregate_metadata.py | |
| - id: 'download-aggregated-outputs' | |
| name: 'Download aggregated outputs' | |
| run: | | |
| gcloud storage cp gs://outbreak-ww-data/aggregate/aggregate_demix.json outputs/aggregate/aggregate_demix.json --billing-project=andersen-lab-primary | |
| gcloud storage cp gs://outbreak-ww-data/aggregate/aggregate_variants.json outputs/aggregate/aggregate_variants.json --billing-project=andersen-lab-primary | |
| gcloud storage cp gs://outbreak-ww-data/aggregate/aggregate_metadata.json outputs/aggregate/aggregate_metadata.json --billing-project=andersen-lab-primary | |
| - id: 'concatenate-outputs' | |
| name: 'Concatenate outputs' | |
| run: | | |
| python scripts/concat_agg_files.py | |
| - id: 'create-demix-by-week' | |
| name: 'Create demix by week' | |
| run: | | |
| python scripts/aggregate_demix_by_week.py | |
| - id: 'upload-outputs' | |
| name: 'Upload Outputs to Cloud Storage' | |
| uses: 'google-github-actions/upload-cloud-storage@v2' | |
| with: | |
| path: 'outputs/' | |
| destination: 'outbreak-ww-data/' | |
| parent: false | |
| project_id: 'andersen-lab-primary' | |
| - name: 'Update processed samples' | |
| run: | | |
| python scripts/update_sample_status.py $BATCH_SIZE | |
| - name: 'Commit and push changes' | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| git remote set-url origin https://github.com/andersen-lab/Freyja-SRA | |
| git add data/all_metadata.csv | |
| git commit -m "Update processed samples" | |
| git push --force | |
| - name: 'Clean workspace' | |
| run: | | |
| rm -rf ${{ github.workspace }}/* |