- name: cnvkit batch test_cnvkit_hybrid
  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
  tags:
    - cnvkit
    - cnvkit/batch
  files:
    - path: output/cnvkit/baits.antitarget.bed
    - path: output/cnvkit/baits.target.bed
      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
    - path: output/cnvkit/reference.cnn
      md5sum: 035d031f54c5f1b43b903da96559b475
    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
      md5sum: 203caf8cef6935bb50b4138097955cb8
    - path: output/cnvkit/test.paired_end.sorted.bintest.cns
      md5sum: 6544d979475def8a9f69ba42a985668d
    - path: output/cnvkit/test.paired_end.sorted.call.cns
      md5sum: f2ca59b4d50b0c317adc526c1b99b622
    - path: output/cnvkit/test.paired_end.sorted.cnr
      md5sum: 7e37d73ab604dbc3fe4ebb56aca9bdc3
    - path: output/cnvkit/test.paired_end.sorted.cns
      md5sum: 060af1aa637ed51812af19bcce24fcfe
    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
      md5sum: 3fe80b6013ffc3e9968345e810158215
    - path: output/cnvkit/test.single_end.sorted.antitargetcoverage.cnn
      md5sum: 203caf8cef6935bb50b4138097955cb8
    - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
      md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7

- name: cnvkit batch test_cnvkit_wgs
  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
  tags:
    - cnvkit
    - cnvkit/batch
  files:
    - path: output/cnvkit/genome.antitarget.bed
    - path: output/cnvkit/genome.bed
      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
    - path: output/cnvkit/genome.target.bed
      md5sum: a13353ae9c8405e701390c069255bbd2
    - path: output/cnvkit/reference.cnn
      md5sum: 1606a85410bfaa79464be6e98699aa83
    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
      md5sum: 203caf8cef6935bb50b4138097955cb8
    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
      md5sum: ff526714696aa49bdc1dc8d00d965266
    - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
      md5sum: 203caf8cef6935bb50b4138097955cb8
    - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
      md5sum: 6544d979475def8a9f69ba42a985668d
    - path: output/cnvkit/test2.paired_end.sorted.call.cns
      md5sum: f6de754c34f780e6befee5b3ff0893f8
    - path: output/cnvkit/test2.paired_end.sorted.cnr
      md5sum: 80318d06c6b095945a0fb0e85e887cbc
    - path: output/cnvkit/test2.paired_end.sorted.cns
      md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
    - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
      md5sum: 6ae6b3fce7299eedca6133d911c38fe1

- name: cnvkit batch test_cnvkit_cram
  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
  tags:
    - cnvkit
    - cnvkit/batch
  files:
    - path: output/cnvkit/genome.antitarget.bed
    - path: output/cnvkit/genome.bed
      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
    - path: output/cnvkit/genome.target.bed
      md5sum: a13353ae9c8405e701390c069255bbd2
    - path: output/cnvkit/reference.cnn
      md5sum: 1606a85410bfaa79464be6e98699aa83
    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
      md5sum: 203caf8cef6935bb50b4138097955cb8
    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
      md5sum: ff526714696aa49bdc1dc8d00d965266
    - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
      md5sum: 203caf8cef6935bb50b4138097955cb8
    - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
      md5sum: 6544d979475def8a9f69ba42a985668d
    - path: output/cnvkit/test2.paired_end.sorted.call.cns
      md5sum: f6de754c34f780e6befee5b3ff0893f8
    - path: output/cnvkit/test2.paired_end.sorted.cnr
      md5sum: 80318d06c6b095945a0fb0e85e887cbc
    - path: output/cnvkit/test2.paired_end.sorted.cns
      md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
    - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
      md5sum: 6ae6b3fce7299eedca6133d911c38fe1

- name: cnvkit batch test_cnvkit_tumoronly
  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
  tags:
    - cnvkit
    - cnvkit/batch
  files:
    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
      md5sum: 3d4d20f9f23b39970865d29ef239d20b
    - path: output/cnvkit/reference_chr21.target-tmp.bed
      md5sum: 657b25dbda8516624efa8cb2cf3716ca
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
      md5sum: 067115082c4af4b64d58c0dc3a3642e4
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
      md5sum: f7caeca04aba28b125ce26b511f42afb
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
      md5sum: d9bdb71ce807051369577ee7f807a40c
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
      md5sum: 2b56aac606ba6183d018b30ca58afcec
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3

- name: cnvkit batch test_cnvkit_tumoronly_cram
  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
  tags:
    - cnvkit
    - cnvkit/batch
  files:
    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
      md5sum: 3d4d20f9f23b39970865d29ef239d20b
    - path: output/cnvkit/reference_chr21.target-tmp.bed
      md5sum: 657b25dbda8516624efa8cb2cf3716ca
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
      md5sum: 067115082c4af4b64d58c0dc3a3642e4
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
      md5sum: f7caeca04aba28b125ce26b511f42afb
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
      md5sum: d9bdb71ce807051369577ee7f807a40c
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
      md5sum: 2b56aac606ba6183d018b30ca58afcec
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3

- name: cnvkit batch test_cnvkit_germline_cram
  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
  tags:
    - cnvkit
    - cnvkit/batch
  files:
    - path: output/cnvkit/multi_intervals.antitarget.bed
      md5sum: 3d4d20f9f23b39970865d29ef239d20b
    - path: output/cnvkit/multi_intervals.target.bed
      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
    - path: output/cnvkit/reference.cnn
      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
      md5sum: 067115082c4af4b64d58c0dc3a3642e4
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
      md5sum: 68b62b75cd91b2ffe5633686fb943490
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
      md5sum: df196edd72613c59186f4d87df3dc4a4
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
      md5sum: 3b4fc0cc73be78f978cfe2422470753e
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f