changed tomtom/glam2 parameters; added min_seq parameter

pipeline.nf

@@ -5,6 +5,8 @@ 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}
 
+params.min_seq = 10
+
 process footprint_extraction {
 
 	tag{name}
@@ -84,7 +86,7 @@ process bed_to_clustered_fasta {
 
     script:
     """
-    Rscript ${path_bin}/bed_to_fasta.R ${bed} ${name}
+    Rscript ${path_bin}/bed_to_fasta.R ${bed} ${name} ${params.min_seq}
     """
 }
 
@@ -107,7 +109,7 @@ process glam2 {
 
     script:
     """
-    glam2 n ${fasta} -O .
+    glam2 n ${fasta} -O . -a 10 -b 20 -z 5
     """
 }
 
@@ -128,7 +130,7 @@ process tomtom {
 
     script:
     """
-    tomtom ${meme} ${jaspar_db} -thresh 0.01 -mi 1 -text | sed '/^#/ d' | sed '/^\$/d' > ${name}_known_motif.tsv
+    tomtom ${meme} ${jaspar_db} -thresh 0.01 -text --norc | sed '/^#/ d' | sed '/^\$/d' > ${name}_known_motif.tsv
     """
 }