rnaseq-nextflow-pipeline/.github/workflows/ci.yml at 6a19ffa9919a176cd0281e92e9a84eb59a44d494 · Ekin-Kahraman/rnaseq-nextflow-pipeline · GitHub

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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"