-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #75 from Krannich479/main
CI for variant calling via Github Actions and CIEVaD
- Loading branch information
Showing
2 changed files
with
142 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters