From 6f6aa9d52632c32fae0f46d47859fed0918a77c9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 26 Dec 2018 19:33:15 -0600
Subject: [PATCH] Update script name, R version and end result.
---
workflow/conf/biohpc.config | 2 +-
workflow/main.nf | 3 +--
workflow/scripts/diff_peaks.R | 6 +-----
3 files changed, 3 insertions(+), 8 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 6c9806f..73bffa1 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -53,7 +53,7 @@ process {
executor = 'local'
}
withName: diffPeaks {
- module = ['R/3.4.1-gccmkl']
+ module = ['R/3.3.2-gccmkl']
cpus = 32
}
withName: motifSearch {
diff --git a/workflow/main.nf b/workflow/main.nf
index 2dbf708..b869164 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -428,7 +428,6 @@ process diffPeaks {
script:
if (noUniqueExperiments.size() == 1) {
"""
- touch design_diffpeak_annotatePeaks.tsv
touch no_diffbind.bed
touch no_diffbind.csv
touch heatmap.pdf
@@ -438,7 +437,7 @@ process diffPeaks {
}
else {
"""
- Rscript $baseDir/scripts/dba.R $designDiffPeaks
+ Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
"""
}
diff --git a/workflow/scripts/diff_peaks.R b/workflow/scripts/diff_peaks.R
index 31ccf72..76caa95 100644
--- a/workflow/scripts/diff_peaks.R
+++ b/workflow/scripts/diff_peaks.R
@@ -8,7 +8,7 @@ args <- commandArgs(trailingOnly=TRUE)
# Check input args
if (length(args) != 1) {
- stop("Usage: dba.r [ annotate_design.tsv ] ", call.=FALSE)
+ stop("Usage: diff_peaks.R [ annotate_design.tsv ] ", call.=FALSE)
}
# Build DBA object from design file
@@ -48,7 +48,3 @@ for (i in c(1:length(data$contrasts))) {
write.table(report,contrast_name,sep="\t",quote=F,row.names=F)
write.table(report[,c(1:3)],contrast_bed_name,sep="\t",quote=F,row.names=F, col.names=F)
}
-
-# Write new design file
-newdesign = data.frame(Condition=new_SampleID, Peaks=new_Peaks)
-write.csv(newdesign,"design_diffpeak_annotatePeaks.csv",row.names=F, quote=F, sep='\t')
--
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