From 28e471cd8bee91ca310448e86f4ec69416670cc0 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Thu, 26 Jan 2017 14:53:19 -0600
Subject: [PATCH] deeptools works
---
astrocyte_package.yml | 3 ++-
workflow/main.nf | 14 ++++++--------
workflow/scripts/runDeepTools.py | 24 ++++++++++++------------
3 files changed, 20 insertions(+), 21 deletions(-)
diff --git a/astrocyte_package.yml b/astrocyte_package.yml
index 9e99a11..6bc210a 100644
--- a/astrocyte_package.yml
+++ b/astrocyte_package.yml
@@ -40,7 +40,8 @@ documentation_files:
# Specify versioned module names to ensure reproducability.
workflow_modules:
- 'deeptools/2.3.5'
- - 'homer/4.7'
+ - 'meme/4.11.1-gcc-openmpi'
+
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
#
diff --git a/workflow/main.nf b/workflow/main.nf
index ffdf4d8..3865d90 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -2,8 +2,8 @@
// Default parameter values to run tests
// params.bams="$baseDir/../test/*.bam"
-params.design="$baseDir/../test/samplesheet.csv"
-// params.genome="/project/shared/bicf_workflow_ref/GRCh37/"
+ params.design="/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/samplesheet.csv"
+ params.genome="/project/shared/bicf_workflow_ref/GRCh37/"
// design_file = file(params.design)
// bams=file(params.bams)
@@ -13,21 +13,19 @@ params.design="$baseDir/../test/samplesheet.csv"
-process peakanno {
+process run_chipseq_analysis {
// publishDir "$baseDir/output", mode: 'copy'
// input:
// file design_file from input
// file annotation Tdx
output:
stdout result
-// set peak_id, file("${pattern}_annotation.xls"), file("${pattern}_peakTssDistribution.png") into peakanno
script:
"""
module load python/2.7.x-anaconda
- module load R/3.2.1-intel
- module load deeptools/2.5.3
- python $baseDir/scripts/process.py
- #Rscript /project/BICF/BICF_Core/bchen4/chipseq_analysis/workflow/scripts/runchipseeker.R
+ module load meme/4.11.1-gcc-openmpi
+ cat $params.design
+ python $baseDir/scripts/process.py -i params.design -g params.genome --top-peak 100
"""
}
diff --git a/workflow/scripts/runDeepTools.py b/workflow/scripts/runDeepTools.py
index 81e02b4..54ee54d 100644
--- a/workflow/scripts/runDeepTools.py
+++ b/workflow/scripts/runDeepTools.py
@@ -24,22 +24,22 @@ def prepare_argparser():
def run_qc(files, controls, labels):
mbs_command = "multiBamSummary bins --bamfiles "+' '.join(files)+" -out sample_mbs.npz"
- #p = subprocess.Popen(mbs_command, shell=True)
+ p = subprocess.Popen(mbs_command, shell=True)
#logging.debug(mbs_command)
- #p.communicate()
- pcor_command = "plotCorrelation -in sample_mbs.npz --corMethod spearman --skipZeros --plotTitle \"Spearman Correlation of Read Counts\" --whatToPlot heatmap --colorMap RdYlBu --plotNumbers --outFileCorMatrix experiment.deeptools.spearmanCorr_readCounts.tab -o experiment.deeptools.heatmap_spearmanCorr_readCounts_v2.png --labels "+" ".join(labels)
+ p.communicate()
+ pcor_command = "plotCorrelation -in sample_mbs.npz --corMethod spearman --skipZeros --plotTitle \"Spearman Correlation of Read Counts\" --whatToPlot heatmap --colorMap RdYlBu --plotNumbers -o experiment.deeptools.heatmap_spearmanCorr_readCounts_v2.png --labels "+" ".join(labels)
#logging.debug(pcor_command)
- #p = subprocess.Popen(pcor_command, shell=True)
- #p.communicate()
+ p = subprocess.Popen(pcor_command, shell=True)
+ p.communicate()
#plotCoverage
pcov_command = "plotCoverage -b "+" ".join(files)+" --plotFile experiment.deeptools_coverage.png -n 1000000 --plotTitle \"sample coverage\" --ignoreDuplicates --minMappingQuality 10"
p = subprocess.Popen(pcov_command, shell=True)
p.communicate()
#draw fingerprints plots
- #for treat,ctrl,name in zip(files,controls,labels):
- # fp_command = "plotFingerprint -b "+treat+" "+ctrl+" --labels "+name+" control --plotFile "+name+".deeptools_fingerprints.png"
- # p = subprocess.Popen(fp_command, shell=True)
- # p.communicate()
+ for treat,ctrl,name in zip(files,controls,labels):
+ fp_command = "plotFingerprint -b "+treat+" "+ctrl+" --labels "+name+" control --plotFile "+name+".deeptools_fingerprints.png"
+ p = subprocess.Popen(fp_command, shell=True)
+ p.communicate()
def bam2bw_wrapper(command):
p = subprocess.Popen(command, shell=True)
@@ -57,8 +57,8 @@ def run_signal(files, labels, genome):
work_pool.join()
cm_command = "computeMatrix scale-regions -R "+gene_bed+" -a 3000 -b 3000 --regionBodyLength 5000 --skipZeros -S *.bw -o samples.deeptools_generegionscalematrix.gz"
- #p = subprocess.Popen(cm_command, shell=True)
- #p.communicate()
+ p = subprocess.Popen(cm_command, shell=True)
+ p.communicate()
hm_command = "plotHeatmap -m samples.deeptools_generegionscalematrix.gz -out samples.deeptools_readsHeatmap.png"
p = subprocess.Popen(hm_command, shell=True)
p.communicate()
@@ -67,7 +67,7 @@ def run(dfile,genome):
#parse dfile, suppose data files are the same folder as design file
dfile = pd.read_csv(dfile)
#QC: multiBamSummary and plotCorrelation
- #run_qc(dfile['bamReads'], dfile['bamControl'], dfile['SampleID'])
+ run_qc(dfile['bamReads'], dfile['bamControl'], dfile['SampleID'])
#signal plots
run_signal(dfile['bamReads'],dfile['SampleID'],genome)
--
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