MPX with IDT Primers #25
Workflow file for this run
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| name: Test SARS-CoV-2 mpx workflow with idt primers | |
| on: [pull_request, workflow_dispatch] | |
| run-name: MPX with IDT Primers | |
| jobs: | |
| mpx_idt: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Download reads | |
| run: | | |
| mkdir reads | |
| cd reads | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_2.fastq.gz | |
| cd ../ | |
| - name: Run Cecret | |
| run: | | |
| nextflow run . -profile docker,mpx_idt -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 | |
| ls cecret* | |
| head cecret*/cecret_results.txt |