From b63eaba2c7dd077a0c4f7cd7c130896f1efb5f9f Mon Sep 17 00:00:00 2001
From: Marius Woeste <mar.w@wwu.de>
Date: Wed, 27 Jul 2022 23:35:09 +0200
Subject: [PATCH] Make gemBS.sh portable on different *nix systems

---
 snakemake_wrapper/scripts/gemBS.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/snakemake_wrapper/scripts/gemBS.sh b/snakemake_wrapper/scripts/gemBS.sh
index ac768ac..8ce20e3 100755
--- a/snakemake_wrapper/scripts/gemBS.sh
+++ b/snakemake_wrapper/scripts/gemBS.sh
@@ -1,10 +1,10 @@
-#!/usr/bin/bash
+#!/usr/bin/env bash
 cd $alignDir
 gemBS prepare -c gemBS.conf -t gemBS_cleaned.csv -o gemBS.json
 gemBS index
 gemBS map
-for file in *.bam; do 
-	mv "$file" "$(echo "$file" | sed s/bam/unmarked.bam/)"; 
+for file in *.bam; do
+	mv "$file" "$(echo "$file" | sed s/bam/unmarked.bam/)";
 done
 rm *.csi *.err *.md5
 exit