CI for variant calling via Github Actions and CIEVaD #12
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| 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 |