inheritFrom: generic-amplicon-with-umi
pipeline:
  - align
  - refineTagsAndSort
  - assemble
  - exportClones
mixins:
  - type: SetSpecies
    species: hsa
  - type: MaterialTypeRNA
  - type: SetTagPattern
    tagPattern: ^(R1:*)\^(MIVBC:N{7:9})(R2:gggagatctctgc*) | ^(MIVBC: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: "CELL to BC"
        matchTags:
          - MIVBC
        newTags:
          - MIBC
        allowOneMismatch: true
        rules:
          - from: GCATCA
            to: BC1
          - from: AGTCGT
            to: BC2
          - from: TCGCAT
            to: BC3
          - from: AGCGTA
            to: BC4
        reportingLevel: VerboseReport
      - type: mapTags
        name: "MIWELL to MIWELLNAME"
        matchTags:
          - MIWELL
        newTags:
          - MIWELLNAME
        allowOneMismatch: true
        rules:
          - from: CTTATGGAAT
            to: A1
          - from: AGAGCACTAG
            to: A2
          - from: TAATGGCAAG
            to: A3
          - from: AGTCAACCAT
            to: A4
          - from: GTATGTAGAA
            to: A5
          - from: TGGATGCTTA
            to: A6
          - from: GTCGATTACA
            to: A7
          - from: TGACTACATA
            to: A8
          - from: GCCATTAGAC
            to: A9
          - from: TAGAATAACG
            to: A10
          - from: TAATGGATCT
            to: A11
          - from: GTGCAACACT
            to: A12
          - from: TCTTACATCA
            to: B1
          - from: TTAGGATAGA
            to: B2
          - from: CCGAAGCGAG
            to: B3
          - from: GGACCAACAG
            to: B4
          - from: TTCCAGGTAA
            to: B5
          - from: TAACAGTGTT
            to: B6
          - from: AGACACATTA
            to: B7
          - from: GCGTTGGTAT
            to: B8
          - from: ACGTCAATAC
            to: B9
          - from: GGTGTACAAG
            to: B10
          - from: ACCTTATGAA
            to: B11
          - from: CGCTGCAGAG
            to: B12
          - from: GTAGAGTCAG
            to: C1
          - from: GGATACCAGA
            to: C2
          - from: CGCACTAATG
            to: C3
          - from: GTAAGGCATA
            to: C4
          - from: GGAATTCCAA
            to: C5
          - from: CTGGATATGT
            to: C6
          - from: CAATCTATGA
            to: C7
          - from: TCTCCATTGA
            to: C8
          - from: ACATGCATAT
            to: C9
          - from: ACGCTAATTA
            to: C10
          - from: CCTTGTTAAT
            to: C11
          - from: GTAGCCATCA
            to: C12
          - from: CTTGTAATTC
            to: D1
          - from: TCCAATTCTA
            to: D2
          - from: GAACAAGTAT
            to: D3
          - from: ACACAATATC
            to: D4
          - from: AACGTTACAT
            to: D5
          - from: CATAACACCA
            to: D6
          - from: ATAGGTATTC
            to: D7
          - from: CCTTCACGTA
            to: D8
          - from: ATTCAGAATC
            to: D9
          - from: GTATTCTCTA
            to: D10
          - from: CCTGATACAA
            to: D11
          - from: AGATGGAATT
            to: D12
          - from: ACACCGTTAA
            to: E1
          - from: CGAAGGTTAA
            to: E2
          - from: ATCGCATATG
            to: E3
          - from: CCAACAACAT
            to: E4
          - from: TCCAAGAATT
            to: E5
          - from: CAACATTCAA
            to: E6
          - from: TATCATGAGA
            to: E7
          - from: AGTTATCACA
            to: E8
          - from: GTAGCATACT
            to: E9
          - from: CTTCAGTTAC
            to: E10
          - from: GATATCCTAA
            to: E11
          - from: AATAGAGCAA
            to: E12
          - from: CTAACTGTAA
            to: F1
          - from: TACCGAACTA
            to: F2
          - from: GGTTATGCTA
            to: F3
          - from: GCTTCCACTA
            to: F4
          - from: AAGTCTTGTA
            to: F5
          - from: TGCTAACTAT
            to: F6
          - from: TAAGACCTAT
            to: F7
          - from: TGGTTAAGAA
            to: F8
          - from: TTGAGAGGAT
            to: F9
          - from: AGTGGATAAT
            to: F10
          - from: GGTATTGAGA
            to: F11
          - from: AGATTGTTAC
            to: F12
          - from: CATGGTCTAA
            to: G1
          - from: GAGACATAAT
            to: G2
          - from: AGCTGTTATA
            to: G3
          - from: CACTTAATCT
            to: G4
          - from: CAGAGTGATA
            to: G5
          - from: GACTTAGAAG
            to: G6
          - from: AGTGAGTGAA
            to: G7
          - from: TGTGATGTAT
            to: G8
          - from: AACATACCTA
            to: G9
          - from: CATACTTGAA
            to: G10
          - from: TGCACGAGAA
            to: G11
          - from: GTGCTATTAA
            to: G12
          - from: TACTAACACA
            to: H1
          - from: AAGCAGATAT
            to: H2
          - from: TTGGATTCAA
            to: H3
          - from: ACCAGTCATT
            to: H4
          - from: CCACCTTACA
            to: H5
          - from: TTCCTCCTTA
            to: H6
          - from: TGAAGTAAGT
            to: H7
          - from: AGCATTAACT
            to: H8
          - from: ACTGAATAGA
            to: H9
          - from: CAGTATCAAT
            to: H10
          - from: ATGAGAACCA
            to: H11
          - from: CAAGTTCATA
            to: H12
        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