✅ Add ci with nf-test #16
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-purple 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: Pull Docker image and cache | |
| run: | | |
| docker pull papaemmelab/purple:v0.1.0 | |
| - name: Run test data | |
| run: | | |
| nextflow run main.nf -profile cloud \ | |
| --tumor TEST \ | |
| --tumorBam `pwd`/tests/data/tumor.bam \ | |
| --refGenome `pwd`/tests/data/reference.fasta \ | |
| --outdir /app/results | |
| - name: Check result | |
| run: | | |
| if [ ! -f /app/results/TEST.purple.purity.tsv ]; then | |
| echo "Result 'TEST.purple.purity.tsv' does not exist" | |
| exit 1 | |
| fi |