From e451422ded2c294f8db40d29239bbbf2116568e4 Mon Sep 17 00:00:00 2001 From: "Andrea Telatin (QIB)" Date: Fri, 5 Nov 2021 17:24:42 +0000 Subject: [PATCH] tree --- bin/dadaist2 | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bin/dadaist2 b/bin/dadaist2 index 43c58f2..6e88679 100755 --- a/bin/dadaist2 +++ b/bin/dadaist2 @@ -99,7 +99,7 @@ my $opt_metadata_separator = "\t"; my $opt_notify = 0; my $opt_crosstalk = 0; my $opt_seqfu = undef; -my $opt_skip_tree = 0; +my $opt_skip_tree = 0; # FASTP Preprocess # To be autocalculated: @@ -156,10 +156,6 @@ my %dependencies = ( 'exporter' => File::Spec->catfile($RealBin, 'dadaist2-exporter') . ' --version', ); -if (not $opt_skip_tree) { - $dependencies{'fasttree'} = 'fasttree 2>&1 | head -n 1 | cut -c 11-'; - $dependencies{'clustalo'} = 'clustalo --version 2>&1'; -} my $parsed = GetOptions( @@ -206,6 +202,12 @@ my $parsed = GetOptions( ) || die " Parameters error, type --help for more info.\n"; die " ERROR: Unexpected parameters: ", join(", ", @ARGV), "\n" if ($ARGV[0]); + +if (not $opt_skip_tree) { + $dependencies{'fasttree'} = 'fasttree 2>&1 | head -n 1 | cut -c 11-'; + $dependencies{'clustalo'} = 'clustalo --version 2>&1'; +} + =pod =head1 PARAMETERS