From 74e367c13ea1a6cb2d246017a976761b04746099 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 4 Jan 2019 12:41:17 -0600
Subject: [PATCH] Fix paried-end quality output options.
---
workflow/main.nf | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 4fa5d9f..e91f56f 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -13,6 +13,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.cutoffRatio = 1.2
+params.extendReadsLen = 100
// Check inputs
if( params.bwaIndex ){
@@ -36,6 +37,7 @@ designFile = params.designFile
genomeSize = params.genomeSize
chromSizes = params.chromSizes
cutoffRatio = params.cutoffRatio
+extendReadsLen = params.extendReadsLen
process checkDesignFile {
@@ -193,7 +195,7 @@ process experimentQC {
script:
"""
- python3 $baseDir/scripts/experiment_qc.py -d $dedupDesign
+ python3 $baseDir/scripts/experiment_qc.py -d $dedupDesign -e $extendReadsLen
"""
}
--
GitLab