finished create_GTF

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}
 	"""
 }