Merge pull request #849 from mgcam/mark_dups4tagzero

Changed mark duplicate method retrieval.

Changes

@@ -1,6 +1,9 @@
 LIST OF CHANGES
 ---------------
 
+ - Ensured mark duplicate method can be inferred for a product with multiple
+   studies (tag zero).
+
 release 68.3.0 (2024-05-24)
  - Removing Tidyp dependency from CI
  - Added 'SampleSheet.csv' file from the top level of the run folder to

lib/npg_pipeline/product/release.pm

@@ -6,6 +6,7 @@ use Data::Dump qw{pp};
 use Moose::Role;
 use List::Util qw{all any};
 use Readonly;
+use Try::Tiny;
 
 with qw{WTSI::DNAP::Utilities::Loggable
         npg_tracking::util::pipeline_config};
@@ -300,7 +301,7 @@ sub bwakit_enable {
   Arg [1]    : npg_pipeline::product
 
   Example    : $obj->markdup_method($product);
-  Description: Return mark duplicate method,
+  Description: Returns mark duplicate method,
                the value might be undefined.
 
   Returntype : Str
@@ -309,7 +310,22 @@ sub bwakit_enable {
 
 sub markdup_method {
   my ($self, $product) = @_;
-  return $self->find_study_config($product)->{markdup_method};
+
+  my $config;
+  try {
+    $config = $self->find_study_config($product);
+  } catch {
+    my $error = $_;
+    if ($error =~ /Multiple[ ]study[ ]ids/xms) {
+      $self->logwarn($error);
+      $self->logwarn('Falling back to the default section of the product config');
+      $config = $self->default_study_config();
+    } else {
+      $self->logcroak($error);
+    }
+  };
+
+  return defined $config ? $config->{markdup_method} : undef;
 }
 
 =head2 staging_deletion_delay
@@ -412,6 +428,8 @@ study:
 
 =item Readonly
 
+=item Try::Tiny
+
 =item WTSI::DNAP::Utilities::Loggable
 
 =item npg_tracking::util::pipeline_config
@@ -430,7 +448,7 @@ study:
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2018,2019,2020,2021,2022 Genome Research Ltd.
+Copyright (C) 2018,2019,2020,2021,2022,2024 Genome Research Ltd.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

t/20-function-seq_alignment.t

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 20;
+use Test::More tests => 21;
 use Test::Exception;
 use Test::Deep;
 use Test::Warn;
@@ -13,7 +13,7 @@ use Log::Log4perl qw/:levels/;
 use JSON;
 use Cwd;
 use List::Util qw/first/;
-use File::Slurp qw/edit_file_lines/;
+use File::Slurp qw/edit_file_lines read_file write_file/;
 
 use Moose::Util qw(apply_all_roles);
 
@@ -1502,7 +1502,7 @@ subtest 'miseq_primer_panel_only' => sub {
   is ($d->command(), $command, 'correct command for MiSeq lane 24135_1 tag index 1');
 };
 
-subtest 'product_release_tests' => sub {
+subtest 'product_release_tests and mark duplicate method' => sub {
   plan tests => 269;
 
   my %test_runs = (
@@ -1572,6 +1572,47 @@ subtest 'product_release_tests' => sub {
   }
 };
 
+subtest 'mark duplicate method for a product with multiple studies' => sub {
+  plan tests => 3;
+
+  my $runfolder_path = join q[/], $dir, q[markdups_test];
+  mkdir $runfolder_path;
+  copy('t/data/miseq/46761_RunInfo.xml', "$runfolder_path/RunInfo.xml") or die 'Copy failed';
+  copy('t/data/miseq/46761_runParameters.xml', "$runfolder_path/runParameters.xml")
+    or die 'Copy failed';
+  my @lines = read_file(q[t/data/miseq/samplesheet_46761_bwa_mem2.csv]);
+  my @data = ();
+  # Change study ID for the first tag.
+  foreach my $value ((split q[,], $lines[2])) {
+    $value =~ s/5556/5557/;
+    push @data, $value;
+  }
+  $lines[2] = join q[,], @data;
+  my $samplesheet = "$runfolder_path/samplesheet_46761.csv";
+  write_file($samplesheet, @lines);
+  local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $samplesheet;
+
+  my $ms_gen = npg_pipeline::function::seq_alignment->new(
+    id_run            => 46761,
+    runfolder_path    => $runfolder_path,
+    conf_path         => 't/data/release/config/seq_alignment',
+    resource          => $default,
+    npg_tracking_schema => undef
+  );
+  my $product;
+  foreach my $p (@{$ms_gen->products->{data_products}}) {
+    if ($p->rpt_list eq '46761:1:0') {
+      $product = $p;
+      last;
+    }
+  }
+
+  is ($product->lims->study_ids, 2, 'tag zero product has two study ids');
+  my $method;
+  lives_ok { $method = $ms_gen->markdup_method($product) }
+    'no error calling markdup_method';
+  is ($method, 'biobambam', 'correct method');
+};
 # test overrides of bwa_mem with bwa-mem2
 #   1) on sample sheet entry without [bwa_mem2] specified in reference name
 #   2) on sample sheet entry without [bwa_mem2] specified in reference name, but setting bwa_mem2 attribute