- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
  command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.f1r2.tar.gz
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 887d54e393510f1d0aa2c33bc6155161
    - path: output/gatk4/test.vcf.gz.tbi

- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
  command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 106c5828b02b906c97922618b6072169
    - path: output/gatk4/test.vcf.gz.tbi

- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
  command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 106c5828b02b906c97922618b6072169
    - path: output/gatk4/test.vcf.gz.tbi

- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
  command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 4f77301a125913170b8e9e7828b4ca3f
    - path: output/gatk4/test.vcf.gz.tbi

- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
  command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: fc6ea14ca2da346babe78161beea28c9
    - path: output/gatk4/test.vcf.gz.tbi