main.yml

name: GitHub Actions CI

on:
  push:
    branches: [ master ]
    paths-ignore:
      - '**.md'
  workflow_dispatch:

jobs:

  
  linux-remote:
    name: Linux test (remote)
    runs-on: ubuntu-latest
    env: 
      EXE: ./src/whisper
      EXE_INDEX: ./src/whisper-index
      REFERENCE: ./example/GCF_904425475.1_MG1655_genomic.fna
      FASTQ_1: ./example/SRR10051130_10k_1.fastq
      FASTQ_2: ./example/SRR10051130_10k_2.fastq
      SAM_PE: ./example/out-pe.sam
      SAM_SE: ./example/out-se.sam

 
    steps:
    - uses: actions/checkout@v2
    - name: make
      run: make -j2 -C ./src
    
    - name: indexing
      run: |
        mkdir temp
        mkdir index
        $EXE_INDEX ecoli $REFERENCE ./index ./temp
           
    - name: mapping PE
      run: |
        $EXE -t 1 -rp -out out-pe ./index/ecoli $FASTQ_1 $FASTQ_2
        diff $SAM_PE <(tail -n+4 out-pe.sam)
        
    - name: mapping SE
      run: |
        $EXE -t 1 -rs -out out-se ./index/ecoli $FASTQ_1
        diff $SAM_SE <(tail -n+4 out-se.sam)
        
    
  #macos-remote:
  #  name: macOS build (remote)
  #  runs-on: macOS-latest

  #  steps:
  #  - uses: actions/checkout@v2
  #  - name: make
  #    run: make -j2 -C ./src