From 16c0daa7d2b30a884f41d24694357bca32eb84f0 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Fri, 21 Apr 2017 15:34:49 -0500
Subject: [PATCH] update path
---
workflow/main.nf | 5 ++---
workflow/scripts/runChipseeker.R | 9 ++++++---
workflow/scripts/runDeepTools.py | 2 +-
workflow/scripts/runMemechip.py | 2 +-
4 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index b2b01cc..bbbb08b 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -3,8 +3,7 @@
params.bams = "$baseDir/../test_data/*.bam"
params.bais = "$baseDir/../test_data/*.bai"
params.peaks = "$baseDir/../test_data/*.broadPeak"
- params.genomepath="/project/shared/bicf_workflow_ref/hg19/"
- species = "hg19"
+ params.genomepath="/project/shared/bicf_workflow_ref/GRCh37"
toppeakcount = 200
design_file = file(params.design)
deeptools_design = Channel.fromPath(params.design)
@@ -88,7 +87,7 @@ process run_chipseeker_diffpeak {
"""
module load python/2.7.x-anaconda
module load R/3.3.2-gccmkl
- Rscript $baseDir/scripts/runChipseeker.R $diffpeak_design_file hg19
+ Rscript $baseDir/scripts/runChipseeker.R $diffpeak_design_file ${params.genomepath}
"""
}
diff --git a/workflow/scripts/runChipseeker.R b/workflow/scripts/runChipseeker.R
index 7f7702f..b968efc 100644
--- a/workflow/scripts/runChipseeker.R
+++ b/workflow/scripts/runChipseeker.R
@@ -7,17 +7,20 @@ args = commandArgs(trailingOnly=TRUE)
#}
library(ChIPseeker)
-if(args[2]=="hg19")
+#Parse the genome path and get genome version
+genome = unlist(strsplit(args[2],"[/]"))[-1]
+
+if(genome=="GRCh37")
{
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
}
-if(args[2]=="mm10")
+if(genome=="GRCm38")
{
library(TxDb.Hsapiens.UCSC.mm10.knownGene)
txdb <- TxDb.Hsapiens.UCSC.mm10.knownGene
}
-if(args[2]=="hg38")
+if(genome=="GRCh38")
{
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
diff --git a/workflow/scripts/runDeepTools.py b/workflow/scripts/runDeepTools.py
index 51757f7..7565517 100644
--- a/workflow/scripts/runDeepTools.py
+++ b/workflow/scripts/runDeepTools.py
@@ -47,7 +47,7 @@ def bam2bw_wrapper(command):
def run_signal(files, labels, genome):
#compute matrix and draw profile and heatmap
- gene_bed = genome+"gene.bed"#"/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/genome/"+genome+"/gene.bed"
+ gene_bed = genome+"/gene.bed"#"/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/genome/"+genome+"/gene.bed"
bw_commands = []
for f in files:
bw_commands.append("bamCoverage -bs 10 -b "+f+" -o "+f.replace("bam","bw"))
diff --git a/workflow/scripts/runMemechip.py b/workflow/scripts/runMemechip.py
index b2a15a3..c600c57 100644
--- a/workflow/scripts/runMemechip.py
+++ b/workflow/scripts/runMemechip.py
@@ -40,7 +40,7 @@ def main():
#run(args.infile, args.genome, args.limit, args.output)
#get Pool ready
dfile = pd.read_csv(args.infile)
- meme_arglist = zip(dfile['Peaks'].tolist(),[args.genome+"genome.2bit"]*dfile.shape[0],[str(args.limit)]*dfile.shape[0],dfile['SampleID'].tolist())
+ meme_arglist = zip(dfile['Peaks'].tolist(),[args.genome+"/genome.2bit"]*dfile.shape[0],[str(args.limit)]*dfile.shape[0],dfile['SampleID'].tolist())
work_pool = Pool(min(12,dfile.shape[0]))
resultList = work_pool.map(run_wrapper, meme_arglist)
work_pool.close()
--
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