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steps.cwl
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steps.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
loadData:
type: File
inputBinding:
position: 1
barcodes:
type: File
inputBinding:
position: 2
features:
type: File
inputBinding:
position: 3
matrix:
type: File
inputBinding:
position: 4
minCells:
type: int
inputBinding:
position: 5
minFeatures:
type: int
inputBinding:
position: 6
projectName:
type: string
inputBinding:
position: 7
pattern:
type: string
inputBinding:
position: 8
filterData:
type: File
inputBinding:
position: 9
nFeatureRNAmin:
type: string
inputBinding:
position: 10
nFeatureRNAmax:
type: string
inputBinding:
position: 11
nCountRNAmin:
type: string
inputBinding:
position: 12
nCountRNAmax:
type: string
inputBinding:
position: 13
percentMTmin:
type: string
inputBinding:
position: 14
percentMTmax:
type: string
inputBinding:
position: 15
normalizeData:
type: File
inputBinding:
position: 16
normalization_method:
type: string
inputBinding:
position: 17
scale_factor:
type: string
inputBinding:
position: 18
margin:
type: string
inputBinding:
position: 19
block_size:
type: string
inputBinding:
position: 20
verbose:
type: string
inputBinding:
position: 21
outputs:
step1Output:
type: File
outputSource: loadData/loaded_data
step11utput:
type: File
outputSource: loadData/plot0
step2Output:
type: File
outputSource: filterData/filtered_data
step22Output:
type: File
outputSource: filterData/plots
step3Output:
type: File
outputSource: normalizeData/normalized_data
steps:
loadData:
run: tools/1_loadData.cwl
in:
script: loadData
barcodes: barcodes
features: features
matrix: matrix
minCells: minCells
minFeatures: minFeatures
projectName: projectName
pattern: pattern
out: [loaded_data,plot0]
filterData:
run: tools/2_filter.cwl
in:
script: filterData
dataFile: loadData/loaded_data
nFeatureRNAmin: nFeatureRNAmin
nFeatureRNAmax: nFeatureRNAmax
nCountRNAmin: nCountRNAmin
nCountRNAmax: nCountRNAmax
percentMTmin: percentMTmin
percentMTmax: percentMTmax
out: [filtered_data,plots]
normalizeData:
run: tools/3_normalization.cwl
in:
script: normalizeData
dataFile: filterData/filtered_data
normalization_method: normalization_method
scale_factor: scale_factor
margin: margin
block_size: block_size
verbose: verbose
out: [normalized_data]