From aa5566a24037ab2c6ddfe3d0ec79afa8077213f3 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 9 Mar 2019 21:50:40 -0600
Subject: [PATCH] Add in skipping of diffBind and motif search.
---
workflow/main.nf | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index a8c5027..f06ebc0 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -17,6 +17,8 @@ params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
params.topPeakCount = 600
+params.skipDiff = false
+params.skipMotif = false
// Check inputs
if( params.bwaIndex ){
@@ -45,6 +47,8 @@ cutoffRatio = params.cutoffRatio
outDir = params.outDir
extendReadsLen = params.extendReadsLen
topPeakCount = params.topPeakCount
+skipDiff = params.skipDiff
+skipMotif = params.skipMotif
// Check design file for errors
process checkDesignFile {
@@ -427,6 +431,9 @@ process motifSearch {
file "*memechip" into motifSearch
file "*narrowPeak" into filteredPeaks
+ when:
+ !skipMotif
+
script:
"""
@@ -456,7 +463,7 @@ process diffPeaks {
file 'normcount_peaksets.txt' into normCountPeaks
when:
- noUniqueExperiments > 1
+ noUniqueExperiments > 1 && !skipDiff
script:
"""
--
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