Fix the coverage report, we were using the samtools flags for decont. instead of mapping #14
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-test CI | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.8.4" | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nf-test test |