mpx_yale #38
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name: Test mpx workflow with yale primers | |
on: [pull_request, workflow_dispatch] | |
run-name: mpx_yale | |
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 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_yale -c .github/workflows/github_actions.config --reads reads | |
ls cecret* | |
head cecret*/cecret_results.txt | |
- name: Clean | |
run: rm -rf work .nextflow* |