inheritFrom: generic-amplicon-with-umi
pipeline:
  - align
  - refineTagsAndSort
  - assemble
  - exportClones
mixins:
  - type: SetSpecies
    species: hsa
  - type: MaterialTypeRNA
  - type: SetTagPattern
    tagPattern: ^(R1:*)\^(UMI:N{7:9})(R2:gggagatctctgc*) | ^(UMI:N{7:9})(R2:cagacagacttgt*)
  - type: LeftAlignmentBoundaryNoPoint
    floating: false
  - type: RightAlignmentBoundaryNoPoint
    floating: false
    geneType: C
  - type: SetClonotypeAssemblingFeatures
    features: [ CDR3 ]
align:
  inheritFrom: generic-amplicon-with-umi
  overrides:
    tagTransformationSteps:
      - type: mapTags
        name: "UMI to BC"
        matchTags:
          - UMI
        newTags:
          - UMIBC
        allowOneMismatch: true
        rules:
          - from: GCATCAN
            to: BC1
          - from: AGTCGTN
            to: BC2
          - from: TCGCATCN
            to: BC3
          - from: AGCGTAGN
            to: BC4
          - from: TACGACTN
            to: BC5
          - from: CTGATGAN
            to: BC6
          - from: CATAGCATN
            to: BC7
          - from: GTAGGCTAN
            to: BC8
        reportingLevel: VerboseReport
refineTagsAndSort:
  runCorrection: false
  parameters:
    correctionPower: 1E-3
    backgroundSubstitutionRate: 1E-3
    backgroundIndelRate: 1E-5
    minQuality: 12
    maxSubstitutions: 2
    maxIndels: 2
    maxTotalErrors: 3
assemble:
  inheritFrom: generic-amplicon
exportClones:
    chains: ALL
    splitFilesBy: [ "chain" ]
    fields:
      - field: "-cloneId"
      - field: "-readCount"
      - field: "-readFraction"
      - field: "-tags"
        args: [ "Molecule" ]
      - field: "-targetSequences"
      - field: "-targetQualities"
      - field: "-vHitsWithScore"
      - field: "-dHitsWithScore"
      - field: "-jHitsWithScore"
      - field: "-cHitsWithScore"
      - field: "-vAlignments"
      - field: "-dAlignments"
      - field: "-jAlignments"
      - field: "-cAlignments"
      - field: "-allNFeaturesWithMinQuality"
      - field: "-allAAFeatures"
      - field: "-defaultAnchorPoints"
qc:
  checks:
    - type: SuccessfullyAlignedReads
      middle: 0.7
      upper: 0.85
    - type: OffTargetReads
      middle: 0.1
      upper: 0.2
    - type: ReadsWithNoVOrJHits
      middle: 0.1
      upper: 0.2
    - type: AlignmentsWithNoAssemblingFeature
      middle: 0.05
      upper: 0.15
    - type: ReadsWithNoBarcode
      middle: 0.1
      upper: 0.2
    - type: ReadsUsedInClonotypes
      middle: 0.7
      upper: 0.9
    - type: AlignmentsDroppedLowQuality
      middle: 0.01
      upper: 0.05