- name: bwamem2 mem single-end
  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
  tags:
    - bwamem2
    - bwamem2/mem
  files:
    - path: ./output/bwamem2/test.bam
    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
      md5sum: b02870de80106104abcb03cd9463e7d8
    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
      md5sum: d097a1b82dee375d41a1ea69895a9216
    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567

- name: bwamem2 mem single-end sort
  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
  tags:
    - bwamem2
    - bwamem2/mem
  files:
    - path: ./output/bwamem2/test.bam
    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
      md5sum: b02870de80106104abcb03cd9463e7d8
    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
      md5sum: d097a1b82dee375d41a1ea69895a9216
    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567

- name: bwamem2 mem paired-end
  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
  tags:
    - bwamem2
    - bwamem2/mem
  files:
    - path: ./output/bwamem2/test.bam
    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
      md5sum: b02870de80106104abcb03cd9463e7d8
    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
      md5sum: d097a1b82dee375d41a1ea69895a9216
    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567

- name: bwamem2 mem paired-end sort
  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
  tags:
    - bwamem2
    - bwamem2/mem
  files:
    - path: ./output/bwamem2/test.bam
    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
      md5sum: b02870de80106104abcb03cd9463e7d8
    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
      md5sum: d097a1b82dee375d41a1ea69895a9216
    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
      md5sum: c32e11f6c859f166c7525a9c1d583567