From c67b71f2da6efc583f06c5dac9e95448f3f563e3 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 18 Mar 2025 09:00:55 +0100
Subject: [PATCH] replace sampleRecord logic in kallisto
---
workflows/kallisto/workflow.cwl | 42 ++++++++++++++-------------------
1 file changed, 18 insertions(+), 24 deletions(-)
diff --git a/workflows/kallisto/workflow.cwl b/workflows/kallisto/workflow.cwl
index 1d020e1..ea6b79d 100644
--- a/workflows/kallisto/workflow.cwl
+++ b/workflows/kallisto/workflow.cwl
@@ -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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