From 77a40f95aa04a99efd6da1e9aefb0c871ecabbf6 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Fri, 3 Mar 2017 15:44:14 -0600
Subject: [PATCH] update R moudle
---
workflow/main.nf | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index f5dc46d..5003783 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -1,8 +1,8 @@
#!/usr/bin/env nextflow
- params.design="$baseDir/../test/samplesheet.csv"
- params.bams = "$baseDir/../test/*.bam"
- params.bais = "$baseDir/../test/*.bai"
- params.peaks = "$baseDir/../test/*.broadPeak"
+ params.design="$baseDir/../test_data/samplesheet.csv"
+ params.bams = "$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"
toppeakcount = 200
@@ -32,7 +32,7 @@
// script:
// """
// module load python/2.7.x-anaconda
-// source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+// module load R/3.3.2-gccmkl
// module load samtools/intel/1.3
// samtools index $index_bam_files
// """
@@ -50,7 +50,7 @@ process run_deeptools {
script:
"""
module load python/2.7.x-anaconda
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load R/3.3.2-gccmkl
module load deeptools/2.3.5
python $baseDir/scripts/runDeepTools.py -i ${params.design} -g ${params.genomepath}}
"""
@@ -72,7 +72,7 @@ process run_diffbind {
script:
"""
module load python/2.7.x-anaconda
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load R/3.3.2-gccmkl
Rscript $baseDir/scripts/runDiffBind.R $diffbind_design_file
"""
}
@@ -87,7 +87,7 @@ process run_chipseeker_diffpeak {
script:
"""
module load python/2.7.x-anaconda
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load R/3.3.2-gccmkl
Rscript $baseDir/scripts/runChipseeker.R $diffpeak_design_file hg19
"""
}
@@ -102,7 +102,7 @@ process run_chipseeker_originalpeak {
script:
"""
module load python/2.7.x-anaconda
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load R/3.3.2-gccmkl
Rscript $baseDir/scripts/runChipseeker.R $design_file ${species}
"""
}
@@ -117,7 +117,7 @@ process run_meme_original {
script:
"""
module load python/2.7.x-anaconda
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load R/3.3.2-gccmkl
module load meme/4.11.1-gcc-openmpi
python $baseDir/scripts/runMemechip.py -i $design_meme -g ${params.genomepath} -l ${toppeakcount}
"""
@@ -133,7 +133,7 @@ process run_meme_diffpeak {
script:
"""
module load python/2.7.x-anaconda
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load R/3.3.2-gccmkl
module load meme/4.11.1-gcc-openmpi
python $baseDir/scripts/runMemechip.py -i $diffpeak_design -g ${params.genomepath} -l ${toppeakcount}
"""
--
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