Mercurial > repos > jdv > nanopolish

comparison nanopolish_variants.pl @ 10:c00a942cfc0b draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 1eeffb2cd0b8115ca185f7fcb2df2920dff33e3b
author jdv
date Mon, 12 Feb 2018 23:59:21 -0500
parents f1141f6a2d65
children 550ac6458c07
comparison
equal deleted inserted replaced
9:f1141f6a2d65 10:c00a942cfc0b
96 push @cmd, '--threads', $n_threads; 96 push @cmd, '--threads', $n_threads;
97 97
98 my @regions :shared; 98 my @regions :shared;
99 99
100 # build region tags to pass to nanopolish 100 # build region tags to pass to nanopolish
101 my $parser = BioX::Seq::Stream->new($fn_genome); 101 if (-s $fn_genome) { # gracefully handle empty inputs
102 while (my $seq = $parser->next_seq) { 102 my $parser = BioX::Seq::Stream->new($fn_genome);
103 push @regions, join( ':', $seq->id, 103 while (my $seq = $parser->next_seq) {
104 join( '-', 1, length($seq) ), 104 push @regions, join( ':', $seq->id,
105 ); 105 join( '-', 1, length($seq) ),
106 );
107 }
106 } 108 }
107 109
108 my @workers; 110 my @workers;
109 for (1..$n_workers) { 111 for (1..$n_workers) {
110 push @workers, threads->create(\&run); 112 push @workers, threads->create(\&run);