added script for process 'footprint_extraction'

pipeline.nf

@@ -58,7 +58,7 @@ process overlap_with_known_TFBS {
 process clustering {
 
 	input:
-	file (faste) from FASTA_for_clustering
+	file (fasta) from FASTA_for_clustering
 
 	output:
 	set name, file ('*.bed') into bed_for_motif_esitmation
@@ -132,7 +132,7 @@ process tomtom {
 }
 
 
-//Joining channels with meme and tsv files. Filter joined channel on linecount.
+//Joining channels with meme and tsv files. Filter joined channel on line count.
 //Only meme-files which corresponding tsv files have linecount <= 1 are writen to next channel.
 for_filter = meme_for_filter.join( tsv_for_filter )
 for_filter
@@ -143,7 +143,7 @@ for_filter
     .into { meme_for_scan; check }
 
 
-//If unknown channel is empty print errormessage
+//If channel 'check' is empty print errormessage
 process check_for_unknown_motifs {
     echo true
 
@@ -160,6 +160,7 @@ process check_for_unknown_motifs {
 }
 
 
+//Get the best(first) Motif from each MEME-file
 process get_best_motif {
 
 	input:
@@ -220,6 +221,8 @@ process create_GTF {
 bed_for_final_filter.combine(gtf_for_uropa).set {uropa_in}
 
 
+// Create configuration file for UROPA.
+// Takes template and replaces bed- and gtf-placeholders with actual paths.
 process create_uropa_config {
 
 	publishDir '/mnt/agnerds/Rene.Wiegandt/10_Master/', mode: 'copy'