schema.yaml

---
dataset_id:
  type: 'String'
  required: true
  help: 'Dataset identifier'
variant_type:
  type: 'List'
  required: true
  help: 'List of germline variant types to be called'
  default:
    - "gSV"
    - "gCNV"
  choices:
    - "gSV"
    - "gCNV"
run_discovery:
  type: 'Bool'
  required: true
  help: 'Identify SVs using Delly/Manta'
  default:
    - true
run_regenotyping:
  type: 'Bool'
  required: true
  help: 'Regenotype SVs/CNVs using Delly'
  default:
    - false
run_delly:
  type: 'Bool'
  required: true
  help: 'Run Delly'
  default:
    - true
run_manta:
  type: 'Bool'
  required: true
  help: 'Run Manta'
  default:
    - true
run_qc:
  type: 'Bool'
  required: true
  help: 'Run QC'
  default:
    - true
output_dir:
  type: 'Path'
  mode: 'w'
  required: true
  help: 'Absolute path to output directory'
reference_fasta:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to a reference FASTA file'
exclusion_file:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to an exclusion file'
mappability_map:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to a mappability file'
map_qual:
  type: 'Integer'
  required: true
  help: 'Minimum Paired-End (PE) mapping quality for Delly'
  default: 20
merged_sites_gSV:
  type: 'Path'
  mode: 'r'
  required: false
  help: 'Absolute path to a BCF/VCF file containing merged gSV sites across samples. Required when `run_regenotyping = true`.'
merged_sites_gCNV:
  type: 'Path'
  mode: 'r'
  required: false
  help: 'Absolute path to a BCF/VCF file containing merged gCNV sites across samples. Required when `run_regenotyping = true`.'
save_intermediate_files:
  type: 'Bool'
  required: true
  help: 'Save intermediate files from the pipeline'
  default:
    - false
base_resource_update:
  type: 'ResourceUpdateNamespace'
  required: false
  help: 'User-defined modifications for adjusting base resource allocations for processes'
  elements:
    memory:
      type: 'ResourceUpdateList'
      required: false
      help: 'List of memory updates'
    cpus:
      type: 'ResourceUpdateList'
      required: false
      help: 'List of CPU updates'
input:
  type: 'InputNamespace'
  required: true
  help: 'Input samples'
  elements:
    BAM:
      type: 'InputBAMNamespace'
      required: true
      help: 'Input BAM for germline SV/CNV calling'
      elements:
        normal:
          type: 'BAMEntryList'
          required: true
          help: 'Input BAM'
        tumor:
          type: 'BAMEntryList'
          required: false
          help: 'Input tumor BAM. Only to be used in exceptional use cases. Remove `normal` BAM if this is used.'