MPX with IDT Primers #113
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 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@master | |
| - 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 -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_1.fastq.gz | |
| wget -q 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 | |
| - name: Clean | |
| run: rm -rf work .nextflow* |