update input order

Kelly-ST-HRI · Jan 24, 2022 · 9d91ddd · 9d91ddd
1 parent bb7e964
commit 9d91ddd
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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