- 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 -c ./tests/modules/gatk4/mutect2/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
    - path: output/gatk4/test.vcf.gz.tbi

- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2
  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/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: 17d2091015d04cbd4a26b7a67dc659e6
    - path: output/gatk4/test.vcf.gz.tbi
    - path: output/gatk4/versions.yml

- 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 -c ./tests/modules/gatk4/mutect2/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 55ed641e16089afb33cdbc478e202d3d
    - path: output/gatk4/test.vcf.gz.tbi
    - path: output/gatk4/versions.yml

- 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 -c ./tests/modules/gatk4/mutect2/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: 55ed641e16089afb33cdbc478e202d3d
    - path: output/gatk4/test.vcf.gz.tbi
    - path: output/gatk4/versions.yml

- 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 -c ./tests/modules/gatk4/mutect2/nextflow.config
  tags:
    - gatk4
    - gatk4/mutect2
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.stats
      md5sum: b569ce66bbffe9588b3d221e821023ee
    - path: output/gatk4/test.vcf.gz.tbi
    - path: output/gatk4/versions.yml

- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/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
    - path: output/gatk4/versions.yml

- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
  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
    - path: output/gatk4/test.vcf.gz.tbi
    - path: output/gatk4/versions.yml