added process create_uropa_config

pipeline.nf

@@ -3,6 +3,7 @@
 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.jaspar_db).into {db_for_motivscan; db_for_tomtom}
+Channel.fromPath(params.config).set {config}
 
 process footprint_extraction {
 
@@ -212,15 +213,23 @@ process create_GTF {
 }
 
 
-process create_UROPA_config  {
+bed_for_final_filter.combine(gtf_for_uropa).set {uropa_in}
+
+
+process create_uropa_config {
+
+	publishDir '/mnt/agnerds/Rene.Wiegandt/10_Master/', mode: 'copy'
 
 	input:
+	set val(bed), val(gtf) from uropa_in.toList()
+	file (conf) from config
 
 	output:
 	file ('uropa.config') into uropa_config
 
 	script:
 	"""
+  	sed -- 's/placeholder_gtf/${gtf}/g; s/placeholder_bed/${bed}/g' ${conf} > uropa.config.final
 	"""
 }