✅ Add ci with nf-test #9
Workflow file for this run
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
name: nf-all-classifiers CI | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
jobs: | |
test_pipeline: | |
runs-on: ubuntu-latest | |
name: Job to run the test workflow | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: nf-core/setup-nextflow@v1 | |
- name: Install nf-test | |
run: | | |
wget -qO- https://code.askimed.com/install/nf-test | bash | |
sudo mv nf-test /usr/local/bin/ | |
- name: Run test data | |
run: | | |
# nf-test run tests/workflow.test | |
mkdir -p /data/results | |
nextflow run main.nf -profile cloud \ | |
--tumor TEST \ | |
--tumorBam tests/data/tumor/tumor.bam \ | |
--refGenome tests/data/ref/genome.fasta \ | |
--loci /data/copy_number/GermlineHetPon.37.vcf.gz \ | |
--gcProfile /data/copy_number/GC_profile.1000bp.37.cnp \ | |
--diploidRegions /data/copy_number/DiploidRegions.37.bed.gz \ | |
--ensemblDataDir /data/common/common \ | |
--genomeVersion V37 \ | |
--outdir /data/results | |
- name: Check result | |
run: | | |
if [ ! -f /data/results/TEST.purple.purity.tsv ]; then | |
echo "Result 'TEST.purple.purity.tsv' does not exist" | |
exit 1 | |
fi |