Update merge_gff.nf

fmalmeida · Sep 16, 2021 · b852917 · b852917
1 parent 5954afb
commit b852917
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/generic/merge_gff.nf b/modules/generic/merge_gff.nf
@@ -12,6 +12,6 @@ process gff_merge {
   """
   echo \"##gff-version 3\" > ${prefix}_merged.gff ;
   bedtools sort -i $gff | bedtools merge -d ${params.bedtools_merge_distance} -s -c 2,3,6,7,8,9 -o distinct,distinct,max,distinct,distinct,distinct \
-  | awk 'BEGIN { FS = "\t"; OFS="\\t" } sub(",",";",\$9) { print \$1,\$4,\$5,\$2+1,\$3,\$6,\$7,\$8,\$9}' >> ${prefix}_merged.gff
+  | awk 'BEGIN { FS = "\t"; OFS="\\t" } { sub(",",";",\$9) ; print \$1,\$4,\$5,\$2+1,\$3,\$6,\$7,\$8,\$9}' >> ${prefix}_merged.gff
   """
 }