VariantCalling.yml

name: VariantCallingBenchmark

on:
  push:
    branches: ["main", "dev", "ci"]
  pull_request:
    branches: ["main"]

jobs:
  VariantCallingBenchmark:
    name: CIEVaD benchmarks
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          channels: bioconda,conda-forge,defaults
          channel-priority: true
          auto-activate-base: true

      - name: Check conda installation
        run: |
          conda info
          conda list
          conda config --show-sources
          conda config --show

      - name: Install nextflow
        run: |
          conda install -c bioconda nextflow
          nextflow -version

      - name: Check CovPipe2 presence
        run: nextflow run CoVpipe2.nf --help
        
      - name: Git checkout CIEVaD + REF
        run: |
            git clone https://github.com/rki-mf1/cievad.git
            pushd cievad
            nextflow run hap.nf --help
            nextflow run eval.nf --help
            wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
            sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
            popd

      - name: Run CIEVaD hap
        run: |
            pushd cievad
            nextflow run hap.nf -profile local,conda --reference MN908947.3.fasta
            ls -la results/simulated_hap*NGSWGS*.fastq
            popd

      - name: Run CovPipe2
        run: |
            # BECAUSE CIEVAD'S DEFAULT IS N=3 SAMPLES
            NB_SAMPLES=3
            echo "sample,fastq_1,fastq_2" > samplesheet.csv
            for s in $(seq 1 $NB_SAMPLES); do echo "hap${s},cievad/results/simulated_hap${s}.NGSWGS.R1.fastq,cievad/results/simulated_hap${s}.NGSWGS.R2.fastq" >> samplesheet.csv; done
            cat samplesheet.csv
            nextflow run CoVpipe2.nf \
              -profile local,conda \
              -w work \
              --output results \
              --reference 'sars-cov-2' \
              --fastq samplesheet.csv --list \
              --primer_version V3

      - name: Prep CIEVaD input
        run: |
            NB_SAMPLES=3
            mkdir -p cievad/callsets
            for s in $(seq 1 $NB_SAMPLES); do ln -sr results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done

      - name: Run CIEVaD eval
        run: |
            pushd cievad
            tree .
            nextflow run eval.nf -profile local,conda --callsets_dir callsets --reference MN908947.3.fasta
            tree results
            popd

      - name: Create Badge variable for average indel F1-score # in personal (non-organisational) git repos the score can be visualized via schneegans' dynamic badge action
        run: |
            INDELS_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "indels" | sed 's/indels,//g')
            INDELS_AVG_F1_ABS=$(echo $INDELS_AVG_F1*100 | bc)
            INDELS_AVG_F1_INT=$(echo $INDELS_AVG_F1_ABS | cut -f 1 -d '.')
            echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
            echo $INDELS_AVG_F1_ABS
            echo $INDELS_AVG_F1_INT
            if [ "$INDELS_AVG_F1_INT" -lt 91 ]; then
              echo "Indels benchmark value decreased since last test! Exiting with status 1."
              exit 1
            else
              echo "Indels benchmark did not drop since last test."
            fi

      #- name: Create Indels Badge
      #  uses: schneegans/dynamic-badges-action@v1.7.0
      #  with:
      #    auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
      #    gistID: 4a0fffafb6e8969ddb31b3100926e9cf
      #    filename: cievad_covpipe2_indels.json # Use test.svg if you want to use the SVG mode.
      #    namedLogo: GitHub
      #    label: Indels F1-score
      #    message: ${{ env.INDELS_SCORE }}%
      #    valColorRange: ${{ env.INDELS_SCORE }}
      #    minColorRange: 0
      #    maxColorRange: 100

      - name: Create Badge variable for average SNV F1-score
        run: |
            SNV_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "SNVs" | sed 's/SNVs,//g')
            SNV_AVG_F1_ABS=$(echo $SNV_AVG_F1*100 | bc)
            SNV_AVG_F1_INT=$(echo $SNV_AVG_F1_ABS | cut -f 1 -d '.')
            echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
            echo $SNV_AVG_F1_ABS
            echo $SNV_AVG_F1_INT
            if [ "$SNV_AVG_F1_INT" -lt 96 ]; then
              echo "SNV benchmark value decreased since last test! Exiting with status 1."
              exit 1
            else
              echo "SNV benchmark did not drop since last test."
            fi

      #- name: Create SNV Badge
      #  uses: schneegans/dynamic-badges-action@v1.7.0
      #  with:
      #    auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
      #    gistID: 87db7a851147867bc3e8857dc643dd15
      #    filename: cievad_covpipe2_SNV.json # Use test.svg if you want to use the SVG mode.
      #    namedLogo: GitHub
      #    label: SNV F1-score
      #    message: ${{ env.SNV_SCORE }}%
      #    valColorRange: ${{ env.SNV_SCORE }}
      #    minColorRange: 0
      #    maxColorRange: 100