From 8fba6bd91c5fce346901a4d16b7c2ea32d705c01 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 21 Mar 2020 10:17:02 -0500
Subject: [PATCH] Add usage statement.
---
workflow/main.nf | 3 +--
workflow/scripts/plot_profile.sh | 30 +++++++++++++++++++++++++++++-
2 files changed, 30 insertions(+), 3 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 90f0c90..66278ca 100644
--- a/workflow/main.nf
+++ b/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
"""
}
diff --git a/workflow/scripts/plot_profile.sh b/workflow/scripts/plot_profile.sh
index 09b15eb..caa7056 100755
--- a/workflow/scripts/plot_profile.sh
+++ b/workflow/scripts/plot_profile.sh
@@ -1,6 +1,17 @@
#!/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
--
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