Revert telo gawk changes

Author: weaglesBio

conf/modules.config

@@ -74,6 +74,7 @@ process {
     // NOTE: GAWK module derivatives - More to come
     //
     withName: 'GAWK_UPPER_SEQUENCE' {
+        ext.args2 = { "'/^>/ {print; next} {print toupper(\$0)}'" } // Convert sequence to uppercase on lines starting with '>'
         ext.prefix = { "${meta.id}_UPPERCASED" }
         ext.suffix = 'fasta'
     }
@@ -85,6 +86,7 @@ process {
     }
 
     withName: 'GAWK_MAP_TELO' {
+        ext.args2 = { "-v OFS=\"\t\" 'BEGIN { sub(/^>/, \"\"); print \$1, \$4, \$5, \$6 }'" }
         ext.prefix   = { "${meta.id}_map_telo" }
         ext.suffix   = 'bed'
     }

subworkflows/local/telo_finder/main.nf

@@ -25,7 +25,7 @@ workflow TELO_FINDER {
     //
     GAWK_UPPER_SEQUENCE(
         reference_tuple,
-        file("${projectDir}/bin/gawk_reformat_intersect.awk"),
+        [],
         false,
     )
     ch_versions     = ch_versions.mix( GAWK_UPPER_SEQUENCE.out.versions )
@@ -72,7 +72,7 @@ workflow TELO_FINDER {
 
     GAWK_MAP_TELO(
         fallback_file,
-        file("${projectDir}/bin/gawk_map_telo.awk"),
+        [],
         false
     )
     ch_versions     = ch_versions.mix( GAWK_MAP_TELO.out.versions )