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

- name: bwa mem single-end sort
  command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
  tags:
    - bwa
    - bwa/mem
  files:
    - path: ./output/bwa/test.bam
    - path: ./output/bwa/bwa/genome.bwt
      md5sum: 0469c30a1e239dd08f68afe66fde99da
    - path: ./output/bwa/bwa/genome.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwa/bwa/genome.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567
    - path: ./output/bwa/bwa/genome.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwa/bwa/genome.sa
      md5sum: ab3952cabf026b48cd3eb5bccbb636d1

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

- name: bwa mem paired-end sort
  command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
  tags:
    - bwa
    - bwa/mem
  files:
    - path: ./output/bwa/test.bam
    - path: ./output/bwa/bwa/genome.bwt
      md5sum: 0469c30a1e239dd08f68afe66fde99da
    - path: ./output/bwa/bwa/genome.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwa/bwa/genome.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567
    - path: ./output/bwa/bwa/genome.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwa/bwa/genome.sa
      md5sum: ab3952cabf026b48cd3eb5bccbb636d1