annotation_example.yaml

pattern:
  - '*.maf'
  - '*.vcf'
  - '*.tsv.gz'

format: 'tsv'
delimiter: 't'

columns:
  - 'by_OpenVariant'
  - 'SAMPLE'
  - 'MUTATION_REF'

annotation:
  - type: 'static'
    field: 'by_OpenVariant'
    value: 'True'

  - type: 'internal'
    field: 'CHROMOSOME'
    fieldSource:
      - 'Chromosome'
      - 'Chr'
      - 'Chrom'
      - 'Chromosome_Name'
      - '#chrom'
    function: "lambda c: c.upper().replace('CHR', '').replace('23', 'X').replace('24', 'Y')"

  - type: 'internal'
    field: 'SAMPLE'
    value: '{icgc_sample_id}_{icgc_specimen_id}'
    fieldSource:
      - ['icgc_sample_id','icgc_specimen_id']

  - type: 'filename'
    field: 'DATASET'
    function: 'lambda x: "{}".format(x.lower()[:-4])'
    regex: '[a-zA-Z0-9]*.'

  - type: 'dirname'
    field: 'PROJECT'
    function: 'lambda x: "{}".format(x.lower())'
    regex: '(*.)'

  - type: 'mapping'
    field: 'MUTATION_REF'
    fieldSource:
      - 'MutationID'
      - 'id'
      - 'Mutation_Id'
    fieldMapping: 'MUTATION_ID'
    fileMapping: 'metadata_mutation.tsv'
    fieldValue: 'REFERENCE'

  - type: 'plugin'
    plugin: 'alteration_type'
    field: 'ALT_TYPE'


exclude:
  - field: 'DATASET'
    value: 'laml'

  - field: 'DATASET'
    value: 'ucs'