From 51142e4a8a25e2a23f089bfed8c7d5dc9a36db41 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 15 Feb 2020 23:09:24 -0600
Subject: [PATCH] update reference.
---
workflow/main.nf | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index f907c73..1d4a7fc 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -98,8 +98,7 @@ skipMotif = params.skipMotif
skipPlotProfile = params.skipPlotProfile
references = params.references
multiqc = params.multiqc
-gtfFile_plotProfile = Channel.fromPath(params.gtf)
-gtfFile_annotPeaks = Channel.fromPath(params.gtf)
+gtfFile = Channel.fromPath(params.gtf)
geneNames = Channel.fromPath(params.geneNames)
// Check design file for errors
@@ -485,7 +484,6 @@ process plotProfile {
input:
file ("*.pooled.fc_signal.bw") from bigwigs.collect()
- file gtf from gtfFile_plotProfile
output:
@@ -498,7 +496,7 @@ process plotProfile {
script:
"""
module load deeptools/2.5.0.1
- bash $baseDir/scripts/plot_profile.sh
+ bash $baseDir/scripts/plot_profile.sh $gtfFile
"""
}
@@ -540,7 +538,6 @@ process peakAnnotation {
input:
file designAnnotatePeaks
- file gtf from gtfFile_annotPeaks
file geneNames
output:
@@ -552,7 +549,7 @@ process peakAnnotation {
"""
module load R/3.3.2-gccmkl
- Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $gtf $geneNames
+ Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $gtfFile $geneNames
"""
}
--
GitLab