From 12f65b9c5ca192e0f69c1fac8a10f61801462bcc Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Fri, 10 Feb 2017 12:20:05 -0600
Subject: [PATCH] astrocyte test done
---
workflow/main.nf | 49 +++++++++++++++++++++++++-----------------------
1 file changed, 26 insertions(+), 23 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 937e9ba..f5dc46d 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -1,7 +1,8 @@
#!/usr/bin/env nextflow
params.design="$baseDir/../test/samplesheet.csv"
params.bams = "$baseDir/../test/*.bam"
- params.peaks = "$baseDir/../test/*/broadPeak"
+ params.bais = "$baseDir/../test/*.bai"
+ params.peaks = "$baseDir/../test/*.broadPeak"
params.genomepath="/project/shared/bicf_workflow_ref/hg19/"
species = "hg19"
toppeakcount = 200
@@ -16,24 +17,26 @@
chipseeker_peaks = Channel.fromPath(params.peaks)
diffbind_bams = Channel.fromPath(params.bams)
diffbind_peaks = Channel.fromPath(params.peaks)
- meme_peaks = Channel.fromPath(params.peaks)
+ meme_peaks = Channel.fromPath(params.peaks)
+ deeptools_bamindex = Channel.fromPath(params.bais)
+ diffbind_bamindex = Channel.fromPath(params.bais)
-process bamindex {
- publishDir "$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
- source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
- 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
+// source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+// module load samtools/intel/1.3
+// samtools index $index_bam_files
+// """
+//}
process run_deeptools {
publishDir "$baseDir/output", mode: 'copy'
@@ -60,12 +63,12 @@ process run_diffbind {
file diffbind_design_file from diffbind_design
file diffbind_bam_files from diffbind_bams.toList()
file diffbind_peak_files from diffbind_peaks.toList()
- file diffbind_ban_indexes from diffbind_bamindex.toList()
+ file diffbind_bam_indexes from diffbind_bamindex.toList()
output:
file "diffpeak.design" into diffpeaksdesign_chipseeker
file "diffpeak.design" into diffpeaksdesign_meme
- file "*diffbind.bed" into diffpeaks_meme
- file "*diffbind.bed" into diffpeaks_chipseeker
+ file "*_diffbind.bed" into diffpeaks_meme
+ file "*_diffbind.bed" into diffpeaks_chipseeker
script:
"""
module load python/2.7.x-anaconda
@@ -93,7 +96,7 @@ process run_chipseeker_originalpeak {
publishDir "$baseDir/output", mode: 'copy'
input:
file design_file from chipseeker_design
- file chipseeker_peak_files from chipseeker_peaks
+ file chipseeker_peak_files from chipseeker_peaks.toList()
output:
stdout result1
script:
@@ -108,7 +111,7 @@ process run_meme_original {
publishDir "$baseDir/output", mode: 'copy'
input:
file design_meme from meme_design
- file meme_peak_files from meme_peaks
+ file meme_peak_files from meme_peaks.toList()
output:
stdout result_meme_original
script:
--
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