From 9d91ddd7e0e50627433834496378f99b1de7d5cf Mon Sep 17 00:00:00 2001
From: Simon Thomas Kelly <simonthomas.kelly@hugp.com>
Date: Mon, 24 Jan 2022 15:13:06 +0900
Subject: [PATCH] update input order

---
 hicup        | 2 +-
 hicup_mapper | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hicup b/hicup
index 004030f..6982d8a 100755
--- a/hicup
+++ b/hicup
@@ -57,8 +57,8 @@ my %config = (
     digest    => '',
     dragen    => '',
     format    => '',
-    index     => '',
     hisat2    => '',
+    index     => '',
     longest   => '',
     re1       => '',
     shortest  => '',
diff --git a/hicup_mapper b/hicup_mapper
index 0bdf329..d909e44 100755
--- a/hicup_mapper
+++ b/hicup_mapper
@@ -66,9 +66,9 @@ my $config_result = GetOptions(
     "bowtie2=s"   => \$config{bowtie2},
     "dragen=s"   => \$config{dragen},
     "hisat2=s"   => \$config{hisat2},
+    "config=s"    => \$config{config},
     "datestamp=s" => \$config{datestamp},
     "example"     => \$config{example},
-    "config=s"    => \$config{config},
     "format=s"    => \$config{format},
     "index=s"     => \$config{index},
     "ligation=s"  => \$config{ligation},    #Hidden flag to pass ligation details from HiCUP so hicup_truncater header can be included in the SAM file