- name: Run bwa index
  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
  tags:
    - bwa
    - bwa_index
  files:
    - path: output/bwa/NC_010473.fa.amb
      md5sum: 942a990ae872f1c0b8d72dda2db405d5
    - path: output/bwa/NC_010473.fa.bwt
      md5sum: 7301b52e2ecb893d429a49fa692447ae
    - path: output/bwa/NC_010473.fa.pac
      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
    - path: output/bwa/NC_010473.fa.sa
      md5sum: a47dcc92e750e2f16fbd979b8ff9538e

- name: Run bwa mem single-end
  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
  tags:
    - bwa
    - bwa_mem
  files:
    - path: output/test_single_end/test.bam
      md5sum: 3ee21210bac387e0335008146e4728bc

- name: Run bwa mem paired-end
  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
  tags:
    - bwa
    - bwa_mem
  files:
    - path: output/test_paired_end/test.bam
      md5sum: 510d8acc6448c07cdacce8e64ec0904c