- name: manta germline
  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
  tags:
    - manta
    - manta/germline
  files:
    - path: output/manta/test.candidate_small_indels.vcf.gz
    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
    - path: output/manta/test.candidate_sv.vcf.gz
    - path: output/manta/test.candidate_sv.vcf.gz.tbi
    - path: output/manta/test.diploid_sv.vcf.gz
    - path: output/manta/test.diploid_sv.vcf.gz.tbi
- name: manta germline target bed
  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
  tags:
    - manta
    - manta/germline
  files:
    - path: output/manta/test.candidate_small_indels.vcf.gz
    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
    - path: output/manta/test.candidate_sv.vcf.gz
    - path: output/manta/test.candidate_sv.vcf.gz.tbi
    - path: output/manta/test.diploid_sv.vcf.gz
    - path: output/manta/test.diploid_sv.vcf.gz.tbi
- name: manta germline target bed jointcalling
  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed_jointcalling -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
  tags:
    - manta
    - manta/germline
  files:
    - path: output/manta/test.candidate_small_indels.vcf.gz
    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
    - path: output/manta/test.candidate_sv.vcf.gz
    - path: output/manta/test.candidate_sv.vcf.gz.tbi
    - path: output/manta/test.diploid_sv.vcf.gz
    - path: output/manta/test.diploid_sv.vcf.gz.tbi