Update: process overlap_with_known_TFBS

pipeline.nf

@@ -1,7 +1,7 @@
 //!/usr/bin/env nextflow
 
 Channel.fromPath(params.input).map {it -> [it.simpleName, it]}.set {bigwig_input}
-Channel.fromPath(params.genome_fasta).into {fa_overlap; fa_scan}
+Channel.fromPath(params.genome_fasta).into {fa_overlap; fa_scan; fa_overlap_2}
 Channel.fromPath(params.jaspar_db).into {db_for_motivscan; db_for_tomtom}
 Channel.fromPath(params.config).set {config}
 
@@ -13,14 +13,14 @@ process footprint_extraction {
 	set name, file (bigWig) from bigwig_input
 
 	output:
-	set name, file ('*.bed') into bed_for_overlapp_with_TFBS
+	set name, file ('*.bed') into bed_for_overlap_with_TFBS
 
 	script:
 	"""
 	"""
 }
 
-
+//Abfrage ob ausgeführt werden muss.
 process extract_known_TFBS {
 
 	input:
@@ -36,16 +36,20 @@ process extract_known_TFBS {
 }
 
 
+bed_for_overlap_with_TFBS.combine(known_TFBS_for_overlap).combine(fa_overlap_2).set {for_overlap}
+
+
 process overlap_with_known_TFBS {
 
 	input:
-	file (TFBS) from known_TFBS_for_overlap
+	set file (bed_footprints), file (bed_motifs), file (fasta) from for_overlap
 
 	output:
 	file ('*.FASTA') into FASTA_for_clustering
 
 	script:
 	"""
+	${path_bin}/compareBed.sh --data ${bed_footprints} --motifs ${bed_motifs} --fasta ${fasta} -o ${name_placeholder} -min ${params.min_size_fp} -max ${params.max_size_fp}
 	"""
 }