Update donut_falls to latest software versions #36
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| name: Test Donut Falls sample sheet all | |
| on: [pull_request, workflow_dispatch] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Get files | |
| run: | | |
| wget --quiet https://zenodo.org/records/10779911/files/df_test_files.tar.gz?download=1 -O dataset.tar.gz | |
| tar -xvf dataset.tar.gz | |
| cp test_files/test_nanopore.fastq.gz test_files/test_nanopore_only.fastq.gz | |
| - name: Run Donut Falls | |
| run: | | |
| docker --version | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/sample_sheet_all.csv | |
| tree donut_falls | |
| - name: Check files | |
| run: | | |
| ls donut_falls/multiqc/multiqc_report.html | |
| cat donut_falls/summary/donut_falls_summary.json |