schema.yaml

---
patient_id:
  type: 'String'
  required: true
  help: 'Patient ID'
dataset_id:
  type: 'String'
  required: true
  help: 'Dataset ID'
aligner:
  type: 'AlignerTool'
  required: true
  help: 'Aligner used to align input BAMs. Provided as <Aligner>-<Aligner-version>'
output_dir:
  type: 'Path'
  mode: 'w'
  required: true
  help: 'Absolute path to output directory'
save_intermediate_files:
  type: 'Bool'
  required: true
  default: false
  help: 'Whether to save intermediate files'
is_emit_original_quals:
  type: 'Bool'
  required: true
  default: true
  help: 'Whether to emit original quality scores after recalibration'
is_DOC_run:
  type: 'Bool'
  required: true
  default: false
  help: 'Whether to run the DepthOfCoverage process, which is very time-consuming for large BAMs'
intervals:
  type: 'String'
  allow_empty: true
  required: true
  help: 'Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS'
scatter_count:
  type: 'Integer'
  required: true
  default: 50
  help: 'How many intervals to divide the genome into for parallelization'
split_intervals_extra_args:
  type: 'String'
  allow_empty: true
  required: false
  help: 'Extra arguments for interval splitting'
gatk_ir_compression:
  type: 'Integer'
  choices: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
  default: 1
  required: false
reference_fasta:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to reference genome fasta'
reference_fasta_fai:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to reference genome fasta index file'
reference_fasta_dict:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to reference genome fasta dictionary'
bundle_mills_and_1000g_gold_standard_indels_vcf_gz:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to Mills and 1000g gold standard INDELs VCF'
bundle_mills_and_1000g_gold_standard_indels_vcf_gz_tbi:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to Mills and 1000g gold standard INDELs VCF index file'
bundle_known_indels_vcf_gz:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to known INDELs VCF'
bundle_known_indels_vcf_gz_tbi:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to known INDELs VCF index file'
bundle_v0_dbsnp138_vcf_gz:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to v0 dbSNP 138 VCF'
bundle_v0_dbsnp138_vcf_gz_tbi:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to v0 dbSNP 138 VCF index file'
bundle_contest_hapmap_3p3_vcf_gz:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to ConEst HapMap 3p3 VCF'
bundle_contest_hapmap_3p3_vcf_gz_tbi:
  type: 'Path'
  mode: 'r'
  required: true
  help: 'Absolute path to ConEst HapMap 3p3 VCF index file'
metapipeline_delete_input_bams:
  type: 'Bool'
  required: true
  default: false
  help: 'Whether to delete the input BAMs'
metapipeline_final_output_dir:
  type: 'String'
  required: false
  help: 'Directory containing final outputs to check before input deletion'
metapipeline_states_to_delete:
  type: 'List'
  required: true
  help: 'List of states for which to delete input BAMs'
  default:
    - 'normal'
    - 'tumor'
  choice:
    - 'normal'
    - 'tumor'
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 BAMs for calling'
      elements:
        normal:
          type: 'BAMEntryList'
          required: false
          help: 'Input normal BAMs'
        tumor:
          type: 'BAMEntryList'
          required: false
          help: 'Input tumor BAMs'
    recalibration_table:
      type: 'RecalibrationTableList'
      required: false
      allow_empty: false
      help: 'List of any available recalibration tables'