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Copy paththermofisher.yaml
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172 lines (155 loc) · 4.47 KB
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"thermofisher-human-oncomine-base":
vendor: "Thermo Fisher"
category: non-generic
abstract: true
inheritFrom: generic-amplicon
pipeline:
- align
- assemble
- exportClones
mixins:
- type: SetSpecies
species: hs
- type: MaterialTypeRNA
- type: LeftAlignmentBoundaryNoPoint
floating: true
- type: SetClonotypeAssemblingFeatures
features: [ "CDR3" ]
"thermofisher-human-rna-trb-oncomine-lr":
label: "Oncomine RNA TCR Beta‑LR Assay"
inheritFrom: thermofisher-human-oncomine-base
defaultChains:
- TCRBeta
mixins:
- type: RightAlignmentBoundaryNoPoint
floating: true
geneType: C
- type: SetClonotypeAssemblingFeatures
features: [ "{CDR1Begin:FR4End}" ]
"thermofisher-human-rna-trb-oncomine-sr":
label: "Oncomine RNA TCR Beta‑SR Assay"
inheritFrom: thermofisher-human-oncomine-base
defaultChains:
- TCRBeta
mixins:
- type: RightAlignmentBoundaryNoPoint
floating: true
geneType: J
"thermofisher-human-dna-trb-oncomine-sr":
label: "Oncomine DNA TCR Beta‑LR Assay"
inheritFrom: thermofisher-human-rna-trb-oncomine-sr
mixins:
- type: MaterialTypeDNA
defaultChains:
- TCRBeta
"thermofisher-human-rna-igh-oncomine-lr":
label: "Oncomine RNA IGH LR Assay"
inheritFrom: thermofisher-human-oncomine-base
defaultChains:
- IGHeavy
mixins:
- type: RightAlignmentBoundaryNoPoint
floating: true
geneType: C
- type: SetClonotypeAssemblingFeatures
features: [ "{CDR1Begin:FR4End}" ]
- type: AddExportClonesField
field: -isotype
insertIndex: -1
args:
- auto
- type: SetSplitClonesBy
geneType: C
value: true
"thermofisher-human-rna-igh-oncomine-sr":
label: "Oncomine RNA IGH SR Assay"
inheritFrom: thermofisher-human-oncomine-base
defaultChains:
- IGHeavy
mixins:
- type: RightAlignmentBoundaryNoPoint
floating: true
geneType: J
"thermofisher-human-dna-igh-oncomine-sr":
label: "Oncomine DNA IGH SR Assay"
inheritFrom: thermofisher-human-rna-igh-oncomine-sr
mixins:
- type: MaterialTypeDNA
defaultChains:
- IGHeavy
"thermofisher-human-dna-bcr-oncomine-pan-clonality":
label: "Oncomine BCR Pan-Clonality Assay"
inheritFrom: thermofisher-human-oncomine-base
defaultChains:
- IGHeavy
- IGLight
mixins:
- type: MaterialTypeDNA
- type: RightAlignmentBoundaryNoPoint
floating: true
geneType: J
"thermofisher-human-dna-igh-oncomine-fr3-j":
label: "Oncomine IGH FR3(d)-J Assay"
inheritFrom: thermofisher-human-dna-bcr-oncomine-pan-clonality
defaultChains:
- IGHeavy
"thermofisher-human-dna-igh-oncomine-fr2-j":
label: "Oncomine IGH FR2-J Assay"
inheritFrom: thermofisher-human-dna-bcr-oncomine-pan-clonality
defaultChains:
- IGHeavy
mixins:
- type: SetClonotypeAssemblingFeatures
features: [ "{CDR2Begin:CDR3End}" ]
"thermofisher-human-dna-igh-oncomine-fr1-j":
label: "Oncomine IGH FR1-J Assay"
inheritFrom: thermofisher-human-dna-bcr-oncomine-pan-clonality
defaultChains:
- IGHeavy
mixins:
- type: SetClonotypeAssemblingFeatures
features: [ "{CDR1Begin:CDR3End}" ]
"thermofisher-human-dna-igh-oncomine-v-leader-j":
label: "Oncomine IGH Leader-J Assay"
inheritFrom: thermofisher-human-dna-bcr-oncomine-pan-clonality
defaultChains:
- IGHeavy
mixins:
- type: SetClonotypeAssemblingFeatures
features: [ "{FR1Begin:CDR3End}" ]
"thermofisher-human-dna-tcr-oncomine-pan-clonality":
label: "Oncomine TCR Pan-Clonality Assay"
inheritFrom: thermofisher-human-dna-bcr-oncomine-pan-clonality
defaultChains:
- TCRBeta
- TCRGamma
"thermofisher-mouse-rna-tcb-ampliseq-sr":
label: "Ion AmpliSeq Mouse TCR Beta‑SR RNA"
inheritFrom: thermofisher-human-rna-trb-oncomine-sr
defaultChains:
- TCRBeta
mixins:
- type: SetSpecies
species: mmu
"thermofisher-mouse-dna-tcb-ampliseq-sr":
label: "Ion AmpliSeq Mouse TCR Beta‑SR DNA"
inheritFrom: thermofisher-mouse-rna-tcb-ampliseq-sr
defaultChains:
- TCRBeta
mixins:
- type: MaterialTypeDNA
"thermofisher-mouse-rna-igh-ampliseq-sr":
label: "Ion AmpliSeq Mouse IGH‑SR RNA"
inheritFrom: thermofisher-human-rna-igh-oncomine-sr
defaultChains:
- IGHeavy
mixins:
- type: SetSpecies
species: mmu
"thermofisher-mouse-dna-igh-ampliseq-sr":
label: "Ion AmpliSeq Mouse IGH‑SR DNA"
inheritFrom: thermofisher-mouse-rna-igh-ampliseq-sr
defaultChains:
- IGHeavy
mixins:
- type: MaterialTypeDNA