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Commit 312c4907 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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collect results in single folder

parent c54d4a87
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......@@ -13,17 +13,20 @@ InputReadsMultipleSamples:
- class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
-
- class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
# -
# - class: File
# path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
# format: edam:format_1930 # FASTQ
numCharsFastqFileName: 6
### Kallisto quant Parameters
isSingle: true
FragmentLength: 200
StandardDeviation: 20
BootstrapSamples: 1
resultsFolder: kallist_results
$namespaces:
edam: https://edamontology.org/
\ No newline at end of file
cwlVersion: v1.2
class: ExpressionTool
doc: |
Takes Files (e.g. from a workflow step) and yields them in a desired directory.
requirements:
- class: InlineJavascriptRequirement
inputs:
files: File[]
destination: string
expression: |
${
return {"outDir": {
"class": "Directory",
"basename": inputs.destination,
"listing": inputs.files
} };
}
outputs:
outDir: Directory
\ No newline at end of file
cwlVersion: v1.2
class: ExpressionTool
doc: |
Takes a directory (e.g. from a workflow step) and yield it in a desired directory.
requirements:
- class: InlineJavascriptRequirement
inputs:
inDir: Directory
destinationDir: string
expression: |
${
return {"outDir": {
"class": "Directory",
"basename": inputs.destinationDir,
"listing": [inputs.inDir]
} };
}
outputs:
outDir: Directory
\ No newline at end of file
......@@ -14,11 +14,11 @@ inputs:
items:
type: array
items: File
numCharsFastqFileName: int?
isSingle: boolean
FragmentLength: double?
StandardDeviation: double?
BootstrapSamples: int?
BootstrapSamples: int?
resultsFolder: string
steps:
index:
......@@ -46,8 +46,15 @@ steps:
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
out: [outFolder]
collectResults:
run: ../_aux-tools/yield-dirInDestination.cwl
scatter: inDir
in:
inDir: quant/outFolder
destinationDir: resultsFolder
out: outDir
outputs:
finalOut:
type: Directory[]
outputSource: quant/outFolder
type: Directory
outputSource: collectResults/outDir
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