NCBench Zenodo Upload #190
Workflow file for this run
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| name: NCBench Zenodo Upload | |
| # This workflow can be triggered manually with the GitHub actions workflow dispatch button. | |
| on: | |
| # upload can only be triggered manually for now | |
| workflow_dispatch: | |
| inputs: | |
| germline_default_agilent: | |
| description: "Trigger NCBench upload" | |
| type: boolean | |
| default: true | |
| jobs: | |
| ncbench-upload: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # TODO: Add in other test profiles | |
| - profile: germline_default_agilent | |
| enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_default_agilent ) }} | |
| steps: | |
| - name: Download pipeline | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Extract Versions | |
| id: extract_versions | |
| run: | | |
| PIPELINE_VERSION=$(awk -F"'" '/manifest {/,/version/ {if(/version/) print $2}' nextflow.config) | |
| echo "PIPELINE_VERSION=${PIPELINE_VERSION}" >> $GITHUB_ENV | |
| echo "PIPELINE_VERSION_NO_DOTS=$(echo $PIPELINE_VERSION | tr -d '.')" >> $GITHUB_ENV | |
| nextflow inspect -profile test_full_germline_ncbench_agilent . --outdir ./inspect >> inspect.json | |
| FASTP_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:FASTP") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "FASTP_VERSION=${FASTP_VERSION}" >> $GITHUB_ENV | |
| BWA_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "BWA_VERSION=${BWA_VERSION}" >> $GITHUB_ENV | |
| BQSR_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "BQSR_VERSION=${BQSR_VERSION}" >> $GITHUB_ENV | |
| DEEPVARIANT_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_DEEPVARIANT:DEEPVARIANT") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "DEEPVARIANT_VERSION=${DEEPVARIANT_VERSION}" >> $GITHUB_ENV | |
| FREEBAYES_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "FREEBAYES_VERSION=${FREEBAYES_VERSION}" >> $GITHUB_ENV | |
| HAPLOTYPECALLER_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "HAPLOTYPECALLER_VERSION=${HAPLOTYPECALLER_VERSION}" >> $GITHUB_ENV | |
| STRELKA_VERSION=$(jq -r '.processes[] | select(.name == "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE") | .container' inspect.json | awk -F':' '{print $NF}' | cut -d "-" -f 1) | |
| echo "STRELKA_VERSION=${STRELKA_VERSION}" >> $GITHUB_ENV | |
| - name: Download files from AWS | |
| uses: keithweaver/[email protected] | |
| if: ${{ matrix.enabled }} | |
| with: | |
| source: "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/test_full_germline_ncbench_agilent/variant_calling" | |
| command: sync | |
| aws_region: eu-west-1 | |
| destination: ./variant_calling | |
| flags: --no-sign-request --include ".vcf.gz" --exclude "g.vcf.gz" | |
| - name: Install requests | |
| run: pip install requests | |
| - name: Upload to zenodo | |
| id: upload_zenodo | |
| env: | |
| # TODO ATTENTION: Use SANDBOX TOKEN during development: ${{ secrets.NCBENCH_CI_TOKEN_SANDBOX }} | |
| ACCESS_TOKEN: ${{ secrets.ZENODO_DEPOSIT }} | |
| PIPELINE_VERSION: ${{ env.PIPELINE_VERSION }} | |
| run: python .github/workflows/upload.py | |
| - name: Store Zenodo deposition ID | |
| run: | | |
| echo "DEPOSITION_ID=$(cat deposition_id.txt)" >> $GITHUB_ENV | |
| # update ncbench config yml | |
| - name: NCBench set config | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.NCBENCH_CI_TOKEN }} | |
| repository: FriederikeHanssen/ncbench-workflow | |
| path: ncbench-workflow/ | |
| ref: main | |
| - name: Install yq | |
| uses: mikefarah/yq@master | |
| - name: Add entry to config | |
| env: | |
| PIPELINE_VERSION_NO_DOTS: ${{ env.PIPELINE_VERSION_NO_DOTS}} | |
| PIPELINE_VERSION: ${{ env.PIPELINE_VERSION }} | |
| FASTP_VERSION: ${{ env.FASTP_VERSION }} | |
| BWA_VERSION: ${{ env.BWA_VERSION }} | |
| BQSR_VERSION: ${{ env.BQSR_VERSION }} | |
| DEEPVARIANT_VERSION: ${{ env.DEEPVARIANT_VERSION }} | |
| FREEBAYES_VERSION: ${{ env.FREEBAYES_VERSION }} | |
| HAPLOTYPECALLER_VERSION: ${{ env.HAPLOTYPECALLER_VERSION }} | |
| STRELKA_VERSION: ${{ env.STRELKA_VERSION }} | |
| DEPOSITION_ID: ${{ env.DEPOSITION_ID }} | |
| run: bash .github/workflows/set_ncbench_config.sh | |
| - name: Commit files | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| cwd: "./ncbench-workflow" | |
| author_name: "FriederikeHanssen" | |
| author_email: "[email protected]" | |
| new_branch: "sarek_${{ env.PIPELINE_VERSION }}" | |
| message: "Add changes" | |
| add: "config/config.yaml" |