- name: gatk4 markduplicates test_gatk4_markduplicates
  command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicates/nextflow.config
  tags:
    - gatk4
    - gatk4/markduplicates
  files:
    - path: output/gatk4/test.bai
      md5sum: 4ac375b5288501c832bc3e4773f06d39
    - path: output/gatk4/test.bam
      md5sum: c1a0d25c5f65514e72aa490326557a88
    - path: output/gatk4/test.bam.metrics

- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
  command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicates/nextflow.config
  tags:
    - gatk4
    - gatk4/markduplicates
  files:
    - path: output/gatk4/test.bai
      md5sum: 832fbc6b3c3266d024fc7131ffd1b45d
    - path: output/gatk4/test.bam
      md5sum: 36909e80bde1aa547fae6382fd35764d
    - path: output/gatk4/test.bam.metrics
      contains:
        - "testN"
        - "2820"

- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_cram_output
  command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_cram_output -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicates/nextflow.config
  tags:
    - gatk4
    - gatk4/markduplicates
  files:
    - path: output/gatk4/test.cram
    - path: output/gatk4/test.cram.crai
      md5sum: 53a329f0828210e317ad81b0e6ca4bc5
    - path: output/gatk4/test.cram.metrics
      contains:
        - "testN"
        - "2820"