- name: picard markduplicates on sorted bam
  command: nextflow run ./tests/software/picard -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: 0ed0bfc94069380334ccd595f6d8207c

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