mixcr/src/main/resources/presets/protocols/nanopore.yaml at develop · milaboratory/mixcr · GitHub

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"generic-ont":
  label: "Oxford Nanopore data"
  category: generic
  inheritFrom: bundle-base
  flags:
    - species
  pipeline:
    - align
    - assemble
    - assembleContigs
    - exportClones
  mixins:
    - type: MaterialTypeRNA
    - type: AssembleContigsWithMaxLength
  align:
    inheritFrom: align-long-read
  assemble:
    inheritFrom: assemble-base
    overrides:
      clnaOutput: true
      cloneAssemblerParameters:
        assemblingFeatures:
          - CDR3
        badQualityThreshold: 0
        minimalQuality: 15
        cloneClusteringParameters:
          clusteringFilter:
            type: advanced
            correctionPower: 0.001
            backgroundSubstitutionRate: 0.01
            backgroundIndelRate: 0.01
  assembleContigs:
    inheritFrom: assembleContigs-base
    overrides:
      parameters:
        alignedRegionsOnly: true
  exportClones:
    inheritFrom: exportClones-base
  qc:
    checks:
      - type: AlignmentsDroppedLowQuality
        middle: 0.5
        upper: 0.7

"generic-ont-with-umi":
  label: "Oxford Nanopore data with UMIs"
  category: generic
  inheritFrom: bundle-base
  flags:
    - species
    - tagPattern
  pipeline:
    - align
    - refineTagsAndSort
    - assemble
    - assembleContigs
    - exportClones
  mixins:
    - type: MaterialTypeRNA
    - type: AssembleContigsWithMaxLength
    - type: AddTagsValidation
      validation:
        type: MustContainTagType
        tagType: Molecule
  align:
    inheritFrom: align-long-read
  refineTagsAndSort:
    inheritFrom: refineTagsAndSort-amplicon-umi-base
  assemble:
    inheritFrom: assemble-with-consensus-base
    overrides:
      clnaOutput: true
      cloneAssemblerParameters:
        assemblingFeatures:
          - CDR3
        badQualityThreshold: 0
        minimalQuality: 15
        cloneClusteringParameters:
          clusteringFilter:
            type: advanced
            correctionPower: 0.001
            backgroundSubstitutionRate: 0.001
            backgroundIndelRate: 0.01
  assembleContigs:
    inheritFrom: assembleContigs-base
    overrides:
      parameters:
        alignedRegionsOnly: true
  exportClones:
    inheritFrom: exportClones-umi-base
  qc:
    checks:
      - type: AlignmentsDroppedLowQuality
        middle: 0.5
        upper: 0.7