From 20f7b1f764cf787f7fa5c29ee9f39a491f40cc13 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Mon, 5 Aug 2024 11:26:45 +0200
Subject: [PATCH] allow to adapt which part of the file name(s) shall be kept
---
runs/kallisto/workflow.yml | 2 ++
workflows/kallisto/kallisto-workflow.cwl | 12 +++++++++++-
2 files changed, 13 insertions(+), 1 deletion(-)
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
index 65f21a5..21d672d 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/workflow.yml
@@ -34,6 +34,8 @@ InputReadsMultipleSamples:
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
+numUnderscoresFileName: 1
+
### Kallisto quant Parameters
isSingle: true
FragmentLength: 200
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index 8a94523..e7f0350 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -14,6 +14,12 @@ inputs:
items:
type: array
items: File
+ # numCharsFileName:
+ # type: int
+ # default: 6
+ numUnderscoresFileName:
+ type: int
+ default: 2
isSingle: boolean
FragmentLength: double?
StandardDeviation: double?
@@ -37,9 +43,13 @@ steps:
scatterMethod: dotproduct
in:
InputReads: InputReadsMultipleSamples
+ # numChars:
+ # source: numCharsFileName
+ numUnderscores: numUnderscoresFileName
QuantOutfolder:
source: InputReadsMultipleSamples
- valueFrom: $(self[0].nameroot.substring(0,6))
+ # valueFrom: $(self[0].nameroot.substring(0, inputs.numChars))
+ valueFrom: $(self[0].nameroot.split('_').slice(0, inputs.numUnderscores).join('_'))
Index: index/index
isSingle: isSingle
FragmentLength: FragmentLength
--
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