Refactoring to one file #10
Workflow file for this run
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| name: Test Donut Falls sample sheet lr with unicycler assembly | |
| 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: Download Unicycler test files | |
| run: | | |
| mkdir reads | |
| # from unicycler test data | |
| wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz | |
| wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz | |
| #wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz | |
| wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz | |
| mv *fastq.gz reads/. | |
| - name: Run Donut Falls | |
| run: | | |
| docker --version | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/ss_lr.csv --assembler unicycler,flye | |
| tree donut_falls | |
| - name: Check files | |
| run: | | |
| ls donut_falls/multiqc/multiqc_report.html | |
| cat donut_falls/summary/donut_falls_summary.json |