From 96beac55085b782d5a817f2f6f31f4c29b42d7ae Mon Sep 17 00:00:00 2001 From: Modupe Adetunji Date: Wed, 26 Feb 2020 15:04:30 -0500 Subject: [PATCH 1/2] changed folder naming scheme --- VariantAnalysisPipeline.pl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/VariantAnalysisPipeline.pl b/VariantAnalysisPipeline.pl index 6e56c08..dbf5afe 100644 --- a/VariantAnalysisPipeline.pl +++ b/VariantAnalysisPipeline.pl @@ -35,7 +35,7 @@ INPUTFILES(); #sort inputfiles #standard error and output file -`mkdir -p $outputfolder`; +`mkdir -p $outputfolder`; print "$outputfolder\n"; chdir ("$outputfolder"); #working from the outputfolder; open(STDOUT, '>', "$std_out") or die "Log file doesn't exist"; open(STDERR, '>', "$std_err") or die "Error file doesn't exist"; @@ -302,16 +302,16 @@ sub INPUTFILES { #sorting the input files foreach (@content) { my $file = basename($_); if($file =~ /.+[_\.][Rr][12].+/) { - $file =~ /(.+)_.*[_\.][Rr][12].+/; $value = $1; + $file =~ /(.+)[_\.][Rr][12].+/; $value = $1; } elsif($file =~ /.+[_\.][12].+/) { - $file =~ /(.+)_.*[_\.][12].+/; $value = $1; + $file =~ /(.+)[_\.][12].+/; $value = $1; } elsif($file =~ /.+[_\.]pe[12]/) { - $file =~ /(.+)_.*[_\.]pe[12].+/; $value = $1; + $file =~ /(.+)[_\.]pe[12].+/; $value = $1; } elsif($file =~ /.+[_\.]PE[12]/) { - $file =~ /(.+)_.*[_\.]PE[12].+/; $value = $1; + $file =~ /(.+)[_\.]PE[12].+/; $value = $1; } else { $value = $1; } From e547c291c0074e0e1993ff9fba4324d8b946710e Mon Sep 17 00:00:00 2001 From: Modupeore O Adetunji Date: Wed, 26 Feb 2020 14:06:54 -0600 Subject: [PATCH 2/2] Update VariantAnalysisPipeline.pl --- VariantAnalysisPipeline.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VariantAnalysisPipeline.pl b/VariantAnalysisPipeline.pl index dbf5afe..eb41a80 100644 --- a/VariantAnalysisPipeline.pl +++ b/VariantAnalysisPipeline.pl @@ -35,7 +35,7 @@ INPUTFILES(); #sort inputfiles #standard error and output file -`mkdir -p $outputfolder`; print "$outputfolder\n"; +`mkdir -p $outputfolder`; chdir ("$outputfolder"); #working from the outputfolder; open(STDOUT, '>', "$std_out") or die "Log file doesn't exist"; open(STDERR, '>', "$std_err") or die "Error file doesn't exist";