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primers

primers #21

Workflow file for this run

name: Test SARS-CoV-2 primers
on: [pull_request, workflow_dispatch]
run-name: primers
jobs:
test:
runs-on: ubuntu-20.04
strategy:
matrix:
primer: [
'midnight_idt_V1',
'midnight_ont_V1',
'midnight_ont_V2',
'midnight_ont_V3',
'ncov_V3',
'ncov_V4',
'ncov_V4.1',
'ncov_V5.3.2',
'mpx_primalseq'
]
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 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 \
--maxcpus 2 \
--medcpus 2 \
--primer_set ${{ matrix.primer }} \
--bcftools_variants false \
--fastqc false \
--ivar_variants false \
--samtools_stats false \
--samtools_coverage false \
--samtools_depth false \
--samtools_flagstat false \
--kraken2 false \
--nextclade false \
--pangolin false \
--freyja false \
--vadr false \
--relatedness false \
--snpdists false \
--iqtree2 false \
--bamsnap false \
--rename false \
--filter false \
--multiqc false
ls cecret*
- name: Clean
run: rm -rf work .nextflow*