From f0b36739bdb22286eccc233fae32c0e1dd21382b Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Tue, 31 Jan 2017 12:13:49 -0600
Subject: [PATCH] nextflow works
---
workflow/main.nf | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 3865d90..b0b7589 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -2,6 +2,7 @@
// Default parameter values to run tests
// params.bams="$baseDir/../test/*.bam"
+ params.testpath="/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/"
params.design="/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/samplesheet.csv"
params.genome="/project/shared/bicf_workflow_ref/GRCh37/"
@@ -23,9 +24,11 @@ process run_chipseq_analysis {
script:
"""
module load python/2.7.x-anaconda
- 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
+ module load meme/4.11.1-gcc-openmpi
+ source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+ module load deeptools/2.3.5
+ module load meme/4.11.1-gcc-openmpi
+ python $baseDir/scripts/process.py -i ${params.design} -g hg19 --top-peak 200
"""
}
--
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