Add usage statement.

workflow/main.nf

@@ -488,7 +488,6 @@ process plotProfile {
   output:
 
   file '*.{png,gz}' into plotProfile
-  file gtf from gtfFile
 
   when:
 
@@ -497,7 +496,7 @@ process plotProfile {
   script:
   """
   module load deeptools/2.5.0.1
-  bash $baseDir/scripts/plot_profile.sh
+  bash $baseDir/scripts/plot_profile.sh -g $gtfFile
   """
 }
 

workflow/scripts/plot_profile.sh

 #!/bin/bash
 #plot_profile.sh
 
+script_name="plot_profile.sh"
+
+#Help function
+usage() {
+  echo "-h  --Help documentation for $script_name"
+  echo "-g  --File path to gtf/bed files"
+  echo "Example: $script_name -g 'genome.gtf'"
+  exit 1
+}
+
+
 raise()
 {
   echo "${1}" >&2
@@ -55,8 +66,25 @@ plot_profile() {
 
 
 run_main() {
+
+  # Parsing options
+  OPTIND=1 # Reset OPTIND
+  while getopts :g:h opt
+      do
+          case $opt in
+              g) gtf=$OPTARG;;
+              h) usage;;
+          esac
+      done
+
+  shift $(($OPTIND -1))
+
+  # Check for mandatory options
+  if [[ -z $gtf ]]; then
+      usage
+  fi
+
 	bws=$(ls *.bw)
-	gtf=$(ls *.gtf *.bed)
 
   check_tools || exit 1