Added Parameter gtf_path. If path is set process create_gtf will be s…

…kipped

pipeline.nf

@@ -9,6 +9,7 @@
 	params.tfbs_path=""
 	params.create_known_tfbs_path = "./"
 	params.help = 0
+	params.get_path=""
 	params.out = "./out/"
 
 //peak_calling
@@ -68,15 +69,16 @@ Required arguments:
 	--genome_fasta		 Path to genome in FASTA-format
 	--motif_db		 Path to motif-database in MEME-format
 	--config		 Path to UROPA configuration file
-	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
-				 Path can be set as tfbs_path in next run. (Default: './')
  	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
 	--out			 Output Directory (Default: './out/')
 
 Optional arguments:
 
 	--help [0|1]		1 to show this help message. (Default: 0)
 	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
+	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
+				 Path can be set as tfbs_path in next run. (Default: './')
+	--gtf_path			Path to gtf-file. If path is set the process which creats a gtf-file is skipped.
 
 	Footprint extraction:
 	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
@@ -578,14 +580,23 @@ process create_GTF {
 	publishDir "${params.out}/gtf/", mode: 'copy'
 
 	output:
-	file ('*.gtf') into gtf_for_uropa
+	file ('*.gtf') into gtf
+
+	when:
+	gtf_path == ""
 
 	script:
 	"""
 	python ${path_bin}/RegGTFExtractor.py ${params.organism} --tissue ${params.tissues} --wd ${path_bin}
 	"""
 }
 
+if (gtf_path == "") {
+	gtf_for_uropa = gtf
+} else {
+	gtf_for_uropa = Channel.fromPath(params.gtf_path)
+}
+
 /*
 bed_for_final_filter.combine(gtf_for_uropa).set {uropa_in}