From 474a510029c16b921084d29a235d4b0c5055e729 Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Tue, 19 Dec 2023 08:46:40 +0000
Subject: [PATCH] Supressed variant calling.

Added a test to test the correctness of passing
the option to teh samplesheet generator.
---
 lib/npg/samplesheet/auto.pm | 3 +--
 t/47-npg_samplesheet_auto.t | 7 ++++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm
index ce007663..e41d05a6 100644
--- a/lib/npg/samplesheet/auto.pm
+++ b/lib/npg/samplesheet/auto.pm
@@ -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
       );
     }
 
diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t
index 9d6a6d31..ca8814ca 100644
--- a/t/47-npg_samplesheet_auto.t
+++ b/t/47-npg_samplesheet_auto.t
@@ -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;