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Supressed variant calling.
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Added a test to test the correctness of passing
the option to teh samplesheet generator.
mgcam committed Dec 19, 2023

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1 parent 58f2257 commit 474a510
Showing 2 changed files with 7 additions and 3 deletions.
3 changes: 1 addition & 2 deletions lib/npg/samplesheet/auto.pm
Original file line number Diff line number Diff line change
@@ -156,8 +156,7 @@ sub process {
$ss = npg::samplesheet::novaseq_xseries->new(
run => $r, id_run => $id_run,
mlwh_schema => $self->mlwh_schema,
align => 1, keep_fastq => 1,
varcall => q(AllVariantCallers)
align => 1, keep_fastq => 1
);
}

7 changes: 6 additions & 1 deletion t/47-npg_samplesheet_auto.t
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
use strict;
use warnings;
use Test::More tests => 14;
use Test::More tests => 15;
use Test::Exception;
use File::Temp qw/ tempdir /;
use Moose::Meta::Class;
use Log::Log4perl qw(:easy);
use File::chdir;
use Perl6::Slurp;

use_ok('npg::samplesheet::auto');

@@ -90,6 +91,10 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema],
my $glob = q[*_47995_NVX1_A_ssbatch98292.csv];
my @files = glob "$dir/samplesheets/$glob";
is (@files, 1, 'one NovaSeqX samplesheet file is generated');
my $compare_file = 't/data/samplesheet/dragen/' .
'231206_47995_NVX1_A_ssbatch98292_align.csv';
is (slurp($files[0]), slurp($compare_file),
'the NovaSeqX samplesheet is generated correctly');
}

1;

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