nanopore #114
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| name: Test SARS-CoV-2 nanopore workflow | |
| on: [pull_request, workflow_dispatch] | |
| run-name: nanopore | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@master | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Download reads | |
| run: | | |
| mkdir nanopore | |
| cd nanopore | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/050/SRR22452250/SRR22452250_1.fastq.gz | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/031/SRR22452231/SRR22452231_1.fastq.gz | |
| cd ../ | |
| - name: Run Cecret | |
| run: | | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --freyja false --nanopore nanopore | |
| ls cecret* | |
| head cecret*/cecret_results.txt | |
| - name: Clean | |
| run: rm -rf work .nextflow* |