Merge branch 'master' of github.com:bystrogenomics/bystro

akotlar · Oct 24, 2024 · ea9470e · ea9470e
2 parents e726f71 + 34f6fa0
commit ea9470e
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diff --git a/perl/dist.ini b/perl/dist.ini
@@ -60,7 +60,7 @@ finder = :ExecFiles
 
 [Test::EOL]
 [Test::EOF]
-strict = 1
+strict = 0
 
 [Test::MinimumVersion]
 

diff --git a/perl/lib/Seq.pm b/perl/lib/Seq.pm
@@ -744,6 +744,12 @@ sub _preparePreprocessorProgram {
 
   my $basename = path($inPath)->basename;
 
+  # Remove all non-alphanumeric characters to make sure
+  # the shell/bash command doens't crash
+  $basename =~ s/[^a-zA-Z0-9-_]/_/g;
+
+  $inPath = quotemeta($inPath);
+
   my $errPath = $self->_workingDir->child( $basename . '.file-log.log' );
 
   #cat is wasteful, but we expect no one reads large uncompressed files