Fix: move inline comment to process header (Nextflow heredoc parser d… #7
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| name: CI | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-java@v4 | |
| with: | |
| distribution: temurin | |
| java-version: 21 | |
| - name: Install Nextflow | |
| run: | | |
| curl -s https://get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Generate test data | |
| run: python test/create_test_data.py | |
| - name: Build test HISAT2 index | |
| run: | | |
| docker run --rm -v "$GITHUB_WORKSPACE/test:/data" \ | |
| quay.io/biocontainers/hisat2:2.2.1--hdbdd923_6 \ | |
| hisat2-build -q /data/genome.fa /data/genome | |
| - name: Run pipeline (test profile) | |
| run: | | |
| nextflow run main.nf \ | |
| -profile test,docker \ | |
| --genome_index "$GITHUB_WORKSPACE/test/genome" \ | |
| --gtf "$GITHUB_WORKSPACE/test/genes.gtf" | |
| - name: Verify outputs | |
| run: | | |
| test -f results/counts/gene_counts.txt | |
| test -f results/deseq2/deseq2_results.csv | |
| test -f results/deseq2/volcano_plot.png | |
| test -f results/deseq2/pca_plot.png | |
| test -f results/multiqc/multiqc_report.html | |
| echo "All outputs verified" |