From ee6e0d7239904d17794695ddc0ed1e5353aa80b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= <rene.wiegandt@mpi-bn.mpg.de>
Date: Tue, 4 Dec 2018 07:13:32 -0500
Subject: [PATCH] finished create_GTF

---
 pipeline.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index fce7066..a8e15dc 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -42,8 +42,6 @@ process extract_known_TFBS {
 }
 
 
-
-
 bed_for_overlap_with_TFBS.combine(known_TFBS_for_overlap).combine(fa_overlap_2).set {for_overlap}
 
 
@@ -64,7 +62,6 @@ process overlap_with_known_TFBS {
 }
 
 
-
 process clustering {
 	conda "${path_env}"
 
@@ -226,11 +223,14 @@ process cluster_quality {
 process create_GTF {
 	conda "${path_env}"
 
+	publishDir 'Path', mode:'copy'
+
 	output:
 	file ('*.gtf') into gtf_for_uropa
 
 	script:
 	"""
+	python ${path_bin}/RegGTFExtractor.py ${params.organism} --tissue ${params.tissues}
 	"""
 }