- 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: 19a4891c3b98d0482dce2253fb28d852

- 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