ncbench.yml

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/aws-s3-github-action@v1.0.0
        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: "FriederikeHanssen@users.noreply.github.com"
          new_branch: "sarek_${{ env.PIPELINE_VERSION }}"
          message: "Add changes"
          add: "config/config.yaml"