From 65bc6b769f9e3eca918b4a6eca0a00fdf386b864 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 24 Jul 2018 23:12:53 -0500
Subject: [PATCH] Covert csv to tsv.
---
workflow/main.nf | 8 ++++----
workflow/scripts/dba.R | 4 ++--
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 40a9990..577903a 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -417,10 +417,10 @@ process diffPeaks {
output:
- file "design_diffpeak_annotatePeaks.csv" into diffPeaksDesignAnnotatePeaks
- file "design_diffpeak_annotatePeaks.csv" into diffPeaksDesignMeme
- file "*_diffbind.bed" into diffpeaks_meme
- file "*_diffbind.bed" into diffpeaks_chipseeker
+ file "design_diffpeak_annotatePeaks.tsv" into diffPeaksDesignAnnotatePeaks
+ file "design_diffpeak_annotatePeaks.tsv" into diffPeaksDesignMeme
+ file "*_diffbind.bed" into diffPeaks
+ file "*_diffbind.csv" into diffPeaksCounts
file '*.pdf' into diffPeaksStats
file 'normcount_peaksets.txt' into normCountPeaks
diff --git a/workflow/scripts/dba.R b/workflow/scripts/dba.R
index 3081db2..42986d2 100644
--- a/workflow/scripts/dba.R
+++ b/workflow/scripts/dba.R
@@ -42,7 +42,7 @@ for (i in c(1:length(data$contrasts))) {
contrast_bed_name = paste(data$contrasts[[i]]$name1,"vs",
data$contrasts[[i]]$name2,"diffbind.bed",sep="_")
contrast_name = paste(data$contrasts[[i]]$name1,"vs",
- data$contrasts[[i]]$name2,"diffbind.xls",sep="_")
+ data$contrasts[[i]]$name2,"diffbind.csv",sep="_")
new_SampleID = c(new_SampleID,paste(data$contrasts[[i]]$name1,"vs",data$contrasts[[i]]$name2,sep="_"))
new_Peaks = c(new_Peaks, contrast_bed_name)
report <- dba.report(data, contrast=i, th=1, bCount=TRUE)
@@ -55,4 +55,4 @@ for (i in c(1:length(data$contrasts))) {
# 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)
+write.csv(newdesign,"design_diffpeak_annotatePeaks.csv",row.names=F, quote=F, sep='\t')
--
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