From d100d9175322d8bb46ceec09b8d656cc3837b6bd Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Fri, 21 Apr 2017 16:35:06 -0500
Subject: [PATCH] fix path and bam indexing
---
workflow/main.nf | 40 ++++++++++++++++----------------
workflow/scripts/runChipseeker.R | 3 ++-
2 files changed, 22 insertions(+), 21 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index bbbb08b..63c2c2b 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -1,7 +1,7 @@
#!/usr/bin/env nextflow
params.design="$baseDir/../test_data/samplesheet.csv"
params.bams = "$baseDir/../test_data/*.bam"
- params.bais = "$baseDir/../test_data/*.bai"
+// params.bais = "$baseDir/../test_data/*.bai"
params.peaks = "$baseDir/../test_data/*.broadPeak"
params.genomepath="/project/shared/bicf_workflow_ref/GRCh37"
toppeakcount = 200
@@ -17,25 +17,25 @@
diffbind_bams = Channel.fromPath(params.bams)
diffbind_peaks = Channel.fromPath(params.peaks)
meme_peaks = Channel.fromPath(params.peaks)
- deeptools_bamindex = Channel.fromPath(params.bais)
- diffbind_bamindex = Channel.fromPath(params.bais)
+// deeptools_bamindex = Channel.fromPath(params.bais)
+// diffbind_bamindex = Channel.fromPath(params.bais)
-//process bamindex {
-// publishDir "$baseDir/output/", mode: 'copy'
-// input:
-// file index_bam_files from index_bams
-// output:
-// file "*bai" into deeptools_bamindex
-// file "*bai" into diffbind_bamindex
-//
-// script:
-// """
-// module load python/2.7.x-anaconda
-// module load R/3.3.2-gccmkl
-// module load samtools/intel/1.3
-// samtools index $index_bam_files
-// """
-//}
+process bamindex {
+ publishDir "$baseDir/output/", mode: 'copy'
+ input:
+ file index_bam_files from index_bams
+ output:
+ file "*bai" into deeptools_bamindex
+ file "*bai" into diffbind_bamindex
+
+ script:
+ """
+ module load python/2.7.x-anaconda
+ module load R/3.3.2-gccmkl
+ module load samtools/intel/1.3
+ samtools index $index_bam_files
+ """
+}
process run_deeptools {
publishDir "$baseDir/output", mode: 'copy'
@@ -102,7 +102,7 @@ process run_chipseeker_originalpeak {
"""
module load python/2.7.x-anaconda
module load R/3.3.2-gccmkl
- Rscript $baseDir/scripts/runChipseeker.R $design_file ${species}
+ Rscript $baseDir/scripts/runChipseeker.R $design_file ${params.genomepath}
"""
}
diff --git a/workflow/scripts/runChipseeker.R b/workflow/scripts/runChipseeker.R
index b968efc..e238a4a 100644
--- a/workflow/scripts/runChipseeker.R
+++ b/workflow/scripts/runChipseeker.R
@@ -8,7 +8,8 @@ args = commandArgs(trailingOnly=TRUE)
library(ChIPseeker)
#Parse the genome path and get genome version
-genome = unlist(strsplit(args[2],"[/]"))[-1]
+path_elements = unlist(strsplit(args[2],"[/]"))
+genome = path_elements[length(path_elements)]
if(genome=="GRCh37")
{
--
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