Add script option

Clinical-Genomics · Aug 18, 2021 · 8c67490 · 8c67490
1 parent ce9b535
commit 8c67490
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Showing 2 changed files with 15 additions and 0 deletions.
diff --git a/lib/MIP/Program/Gnu/Software/Gnu_awk.pm b/lib/MIP/Program/Gnu/Software/Gnu_awk.pm
@@ -35,6 +35,7 @@ sub gnu_awk {
 ##         : $filehandle             => Filehandle to write to
 ##         : $infile_path            => Infile path
 ##         : $outfile_path           => Outfile path
+##         : $script                 => Script to process infile with
 ##         : $stderrfile_path        => Stderrfile path
 ##         : $stderrfile_path_append => Append stderr info to file
 ##         : $stdoutfile_path        => Stdoutfile path
@@ -46,6 +47,7 @@ sub gnu_awk {
     my $filehandle;
     my $infile_path;
     my $outfile_path;
+    my $script;
     my $stderrfile_path;
     my $stderrfile_path_append;
     my $stdoutfile_path;
@@ -64,6 +66,10 @@ sub gnu_awk {
             store       => \$outfile_path,
             strict_type => 1,
         },
+        script => {
+            strict_type => 1,
+            store       => \$script
+        },
         stderrfile_path        => { store => \$stderrfile_path,        strict_type => 1, },
         stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
         stdoutfile_path        => {
@@ -90,6 +96,11 @@ sub gnu_awk {
         push @commands, $infile_path;
     }
 
+    if ($script) {
+
+        push @commands, $script;
+    }
+
     ## Outfile
     if ($outfile_path) {
 

diff --git a/t/gnu_awk.t b/t/gnu_awk.t
@@ -134,6 +134,10 @@ my %specific_argument = (
         input           => q{outfile.test},
         expected_output => q{>outfile.test},
     },
+    script => {
+        input           => q{script.test},
+        expected_output => q{script.test},
+    },
 );
 
 ## Coderef - enables generalized use of generate call