Replaced ROSE with bedtools workflow

conf/modules.config

@@ -28,6 +28,53 @@ process {
         ext.suffix = "bed"
     }
 
+    withName: FILTER_CONVERT_GTF {
+        ext.args = {"'BEGIN {OFS = \"\\t\"} \$3 == \"transcript\" {print \$1, \$4-1, \$4, \$1 \":\" \$4-1 \"-\" \$4, \$6, \$7}'"}
+        ext.suffix = "bed"
+    }
+
+    withName: SORT_BED {
+        ext.args = "-k1,1 -k2,2n"
+        ext.prefix = {"${meta.id}_sorted"}
+        ext.suffix = "bed"
+    }
+
+    withName: CONSTRUCT_TSS {
+        ext.args = "-b 2500"
+        ext.prefix = "tss"
+    }
+
+    withName: FILTER_PREDICTIONS {
+        ext.args = "-A -f 1"
+        ext.prefix = {"${meta.id}_filtered"}
+    }
+
+    withName: STITCHING {
+        ext.args = "-d 12500"
+        ext.prefix = {"${meta.id}_stitched"}
+    }
+
+    withName: TSS_OVERLAP {
+        ext.args = "-c"
+        ext.prefix = {"${meta.id}_tss-overlap-counts"}
+    }
+
+    withName: FILTER_OVERLAPS {
+        ext.args = {"'BEGIN {OFS = \"\\t\"} \$NF >= 2 {print \$1, \$2, \$3}'"}
+        ext.prefix = {"${meta.id}_overlap"}
+    }
+
+    withName: UNSTITCHED_REGIONS {
+        ext.args = "-F 1"
+        ext.prefix = {"${meta.id}_original_regions"}
+    }
+
+    withName: CONCAT_AND_SORT {
+        ext.args = "-k1,1 -k2,2n"
+        ext.prefix = {"${meta.id}_stitched"}
+        ext.suffix = "bed"
+    }
+
     withName: BEDTOOLS_SORT {
         ext.prefix = {"${meta.id}.sorted"}
     }
@@ -62,10 +109,6 @@ process {
         ext.prefix = {"${meta.id}_control"}
     }
 
-    withName: UCSC_GTFTOGENEPRED {
-        ext.args = "-genePredExt"
-    }
-
     withName: ".*DYNAMITE:FILTER" {
         ext.args = {"'BEGIN{OFS=\"\\t\"} NR==1 || (\$2 >= ${params.dynamite_min_regression} || \$2 <= -${params.dynamite_min_regression} )'"}
         ext.prefix = {"${meta.id}.filtered"}