- name: picard markduplicates on sorted bam
  command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
  tags:
    - picard
    - picard/markduplicates
  files:
    - path: ./output/picard/test.MarkDuplicates.metrics.txt
    - path: ./output/picard/test.bam
      md5sum: fe8ed25b4bd25be0cc7a8730fc3b2f30

- name: picard markduplicates on unsorted bam
  command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
  tags:
    - picard
    - picard/markduplicates
    - should fail
  exit_code: 1