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Commit c67b71f2 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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replace sampleRecord logic in kallisto

parent 43934494
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......@@ -8,20 +8,18 @@ requirements:
inputs:
IndexInput: File[]
InputReadsMultipleSamples:
type:
sampleRecord:
type:
type: array
items:
type: array
items: File
# numCharsFileName:
# type: int
# default: 6
numUnderscoresFileName:
type: int
default: 2
items:
type: record
fields:
readsOfOneSample:
type: File[]
sampleName:
type: string?
isSingle: boolean
FragmentLength: double?
FragmentLength: double?
StandardDeviation: double?
BootstrapSamples: int?
resultsFolder: string
......@@ -31,28 +29,24 @@ steps:
run: kallisto-index.cwl
in:
InputFiles: IndexInput
IndexName:
IndexName:
source: IndexInput
valueFrom: $(self[0].nameroot)
out: [index]
quant:
run: kallisto-quant.cwl
scatter:
- InputReads
- QuantOutfolder
scatter: [InputReads, QuantOutfolder]
scatterMethod: dotproduct
in:
InputReads: InputReadsMultipleSamples
# numChars:
# source: numCharsFileName
numUnderscores: numUnderscoresFileName
InputReads:
source: sampleRecord
valueFrom: $(self.readsOfOneSample)
QuantOutfolder:
source: InputReadsMultipleSamples
# valueFrom: $(self[0].nameroot.substring(0, inputs.numChars))
valueFrom: $(self[0].nameroot.split('_').slice(0, inputs.numUnderscores).join('_'))
source: sampleRecord
valueFrom: $(self.sampleName)
Index: index/index
isSingle: isSingle
FragmentLength: FragmentLength
FragmentLength: FragmentLength
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
out: [outFolder]
......
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