strepA.yml

name: Test Grandeur workflow with Group A Strep

on: [pull_request, workflow_dispatch]

jobs:

  test:
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          lfs: true

      - name: Checkout LFS objects
        run: git lfs checkout
            
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
          
      - name: Run Grandeur
        run: |
          docker --version
          
          mkdir fastas 
          for accession in GCA_001412635.1_ASM141263v1 GCA_016724885.1_ASM1672488v1 GCA_900475035.1_41965_F01
          do
            all=$(echo $accession | cut -f 2 -d "_")
            fir=$(echo $all | cut -c 1-3)
            mid=$(echo $all | cut -c 4-6)
            end=$(echo $all | cut -c 7-9)
            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/${fir}/${mid}/${end}/${accession}/${accession}_genomic.fna.gz
            gzip -d ${accession}_genomic.fna.gz
            mv ${accession}_genomic.fna fastas/.
          done

          nextflow run . -profile docker --maxcpus 2 --medcpus 2
          cat grandeur/grandeur_summary.tsv

      - name: Check Strep pneumo file
        run: |
          for file in grandeur/emmtyper/emmtyper_summary.tsv
          do
            head $file
            wc -l $file
          done