Download wastewater fastq #103
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 SARS-CoV-2 workflow on wastewater | |
| on: [pull_request, workflow_dispatch] | |
| run-name: Download wastewater fastq | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@master | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run Cecret | |
| run: | | |
| docker --version | |
| mkdir single_reads | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR194/096/SRR19433296/SRR19433296.fastq.gz | |
| mv *fastq.gz single_reads/. | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --primer_set ncov_V3 --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 | |
| ls cecret* | |
| cat cecret*/cecret_results.txt | |
| head cecret/freyja/aggregated-freyja.tsv | |
| - name: Clean | |
| run: rm -rf work .nextflow* |