test_primers.yml

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'
                ]

    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 \
                --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*