- name: Run picard mergesamfiles
  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
  tags:
    - picard
    - picard_mergesamfiles
  files:
    - path: output/picard/test.bam
      md5sum: a9c8a28d1aac362df5973ba2d9923f86

- name: Run picard collectmultiplemetrics
  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
  tags:
    - picard
    - picard_collectmultiplemetrics
  files:
    # These can't be md5'd consistently
    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics

- name: Run picard MarkDuplicates
  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates -c tests/config/nextflow.config
  tags:
    - picard
    - picard_markduplicates
  files:
    - path: output/picard/test.MarkDuplicates.metrics.txt
    - path: output/picard/test.bam
      md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0

- name: Run picard MarkDuplicates without a sorted bam file so it fails
  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
  tags:
    - picard
    - picard_markduplicates
    - should fail
  exit_code: 1