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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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1 merge request!1Cwl
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...@@ -13,17 +13,20 @@ InputReadsMultipleSamples: ...@@ -13,17 +13,20 @@ InputReadsMultipleSamples:
- class: File - class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ format: edam:format_1930 # FASTQ
- # -
- class: File # - class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ # format: edam:format_1930 # FASTQ
numCharsFastqFileName: 6 numCharsFastqFileName: 6
### Kallisto quant Parameters ### Kallisto quant Parameters
isSingle: true isSingle: true
FragmentLength: 200 FragmentLength: 200
StandardDeviation: 20 StandardDeviation: 20
BootstrapSamples: 1 BootstrapSamples: 1
resultsFolder: kallist_results
$namespaces: $namespaces:
edam: https://edamontology.org/ 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: ...@@ -14,11 +14,11 @@ inputs:
items: items:
type: array type: array
items: File items: File
numCharsFastqFileName: int?
isSingle: boolean isSingle: boolean
FragmentLength: double? FragmentLength: double?
StandardDeviation: double? StandardDeviation: double?
BootstrapSamples: int? BootstrapSamples: int?
resultsFolder: string
steps: steps:
index: index:
...@@ -46,8 +46,15 @@ steps: ...@@ -46,8 +46,15 @@ steps:
StandardDeviation: StandardDeviation StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples BootstrapSamples: BootstrapSamples
out: [outFolder] out: [outFolder]
collectResults:
run: ../_aux-tools/yield-dirInDestination.cwl
scatter: inDir
in:
inDir: quant/outFolder
destinationDir: resultsFolder
out: outDir
outputs: outputs:
finalOut: finalOut:
type: Directory[] type: Directory
outputSource: quant/outFolder outputSource: collectResults/outDir
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