From 58edd844140b3e03c0a72f8239acfacd22724378 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Mon, 21 Nov 2016 13:33:18 -0600
Subject: [PATCH] add scripts folder

---
 workflow/main.nf | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/workflow/main.nf b/workflow/main.nf
index 5a77874..7532c0b 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -1,14 +1,9 @@
 #!/usr/bin/env nextflow
 	
 // Default parameter values to run tests
-params.fastqs="$baseDir/../test_data/*.fastq.gz"
+params.bams="$baseDir/../test_data/*.fastq.gz"
 params.design="$baseDir/../test_data/design.pe.txt"
 params.genome="/project/shared/bicf_workflow_ref/GRCh38/"
-params.markdups="mark"
-params.stranded="0"
-params.pairs="pe"
-params.geneset = 'h.all.v5.1.symbols.gmt'
-params.align = 'hisat'
 
 design_file = file(params.design)
 fastqs=file(params.fastqs)
-- 
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