- name: bwa mem single-end
  command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
  tags:
    - bwa
    - bwa_mem
    - bwa_mem_single_end
  files:
    - path: ./output/bwa/test.bam
      md5sum: c0d98ef222409eca3b7347bfd91484ba
    - path: ./output/bwa/bwa/test_genome.bwt
      md5sum: 0469c30a1e239dd08f68afe66fde99da
    - path: ./output/bwa/bwa/test_genome.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwa/bwa/test_genome.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567
    - path: ./output/bwa/bwa/test_genome.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwa/bwa/test_genome.sa
      md5sum: ab3952cabf026b48cd3eb5bccbb636d1

- name: bwa mem paired-end
  command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
  tags:
    - bwa
    - bwa_mem
    - bwa_mem_paired_end
  files:
    - path: ./output/bwa/test.bam
      md5sum: dcb1c0d42496b582ddb4e8e892b47c4e
    - path: ./output/bwa/bwa/test_genome.bwt
      md5sum: 0469c30a1e239dd08f68afe66fde99da
    - path: ./output/bwa/bwa/test_genome.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwa/bwa/test_genome.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567
    - path: ./output/bwa/bwa/test_genome.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwa/bwa/test_genome.sa
      md5sum: ab3952cabf026b48cd3eb5bccbb636d1