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: 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 |