Merge pull request #967 from mgcam/application_type4ultimagen

Assigned application_type property for Ultimagen sample.

Author: marcomoscasgr

Changes

@@ -8,6 +8,9 @@ LIST OF CHANGES FOR NPG-QC PACKAGE
    reads. This fixes a number of downstream calculations.
  - Added reporting of MQC outcomes for Ultimagen runs.
  - SeqQC - retrieval of LIMS data for Ultimagen runs is added.
+ - Added application_type attribute to npg_qc::ultimagen::sample. Extended
+   npg_qc::ultimagen::library_info parser to assign this attribute from
+   values in [RunID]_LibraryInfo.xml file in the Ultimagen run folder.
 
 release 76.1.0 (2026-02-04)
  - PDL version 2.068 is no longer available on CPAN. Switched to the default

bin/ultimagen_runstats_parser.pl

@@ -17,7 +17,7 @@
 
 =head1 NAME
 
-parse_ultima_stats.pl
+  ultimagen_runstats_parser.pl
 
 =head1 CONFIGURATION
 
@@ -35,7 +35,7 @@ =head1 DESCRIPTION
 
 =head1 USAGE
 
-  parse_ultima_stats.pl --runfolder_path <runfolder> --qc_output_dit <folder> --id_run <run_id>
+  ultimagen_runstats_parser.pl --runfolder_path <runfolder> --qc_output_dir <folder> --id_run <run_id>
 
 =head1 SUBROUTINES/METHODS
 
@@ -92,8 +92,6 @@ =head1 DEPENDENCIES
 
 =head1 INCOMPATIBILITIES
 
-Works for relatively recent runs, post August 2024.
-
 =head1 BUGS AND LIMITATIONS
 
 =head1 AUTHOR
@@ -102,7 +100,7 @@ =head1 AUTHOR
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2025 Genome Research Ltd.
+Copyright (C) 2025, 2026 Genome Research Ltd.
 
 This file is part of NPG.
 

lib/npg_qc/ultimagen/library_info.pm

@@ -67,7 +67,7 @@ sub _build_xml_doc {
 
 =head2 application
 
-Ultima Genomics application name as defined in teh input file. Might be undefined. 
+Ultima Genomics application name as defined in the input file. Might be undefined. 
 
 =cut
 
@@ -134,12 +134,25 @@ sub _build_samples {
   my @samples = ();
   foreach my $se (@{$self->sample_elements}) {
     my ($sample_id, $lib_name) = split /@/smx, $se->getAttribute('Id');
-    push @samples, npg_qc::ultimagen::sample->new(
+    my $init = {
       id => $sample_id,
       library_name => $lib_name,
       index_label => $se->getAttribute('Index_Label'),
-      index_sequence => $se->getAttribute('Index_Sequence')
-    );
+      index_sequence => $se->getAttribute('Index_Sequence'),
+    };
+    my @app_type_values =
+      map  { $_->getAttribute('Value') }
+      grep { $_->getAttribute('Name') eq 'application_type' }
+      grep { ref $_ eq 'XML::LibXML::Element' }
+      $se->childNodes();
+    if (@app_type_values == 1) {
+      $init->{application_type} = $app_type_values[0];
+    } elsif (@app_type_values > 1) {
+      croak 'Multiple application type values for index label '
+        . $init->{index_label};
+    }
+
+    push @samples, npg_qc::ultimagen::sample->new($init);
   }
   return \@samples;
 }
@@ -195,4 +208,4 @@ GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-=cut
+=cut

lib/npg_qc/ultimagen/sample.pm

@@ -78,6 +78,19 @@ has 'index_sequence' => (
   required => 1,
 );
 
+=head2 application_type
+
+Manufacturer's name for the pipeline/tool which was used on-board to
+produce the data. Optional, can be undefined.
+
+=cut
+
+has 'application_type' => (
+  isa      => 'Maybe[Str]',
+  is       => 'ro',
+  required => 0,
+);
+
 =head2 tag_index
 
 NPG tag index, derived from C<index_label> attribute.

t/30-ultimagen-sample_retriever.t

@@ -5,7 +5,7 @@ with 'npg_qc::ultimagen::sample_retriever';
 package main_test;
 use strict;
 use warnings;
-use Test::More tests => 9;
+use Test::More tests => 28;
 use Test::Exception;
 
 use_ok('sample_retriever_test');
@@ -16,21 +16,37 @@ throws_ok { sample_retriever_test->new()->get_samples() }
   qr/Either runfolder_path or manifest_path should be set/,
   'error if no attributes are set';
 
-my $samples_from_li = sample_retriever_test->new(
+my $samples_li = sample_retriever_test->new(
   runfolder_path => $rf
 )->get_samples();
-my $samples_from_ma = sample_retriever_test->new(
+is (scalar @{$samples_li}, 8, 'returned eight samples');
+
+my $samples_ma = sample_retriever_test->new(
   runfolder_path => $rf,
   manifest_path => "${rf}/manifest.csv"
 )->get_samples();
+is (scalar @{$samples_ma}, 8, 'returned eight samples');
+
+for my $sample (($samples_li->[0], $samples_ma->[0])) {
+  is ($sample->id(), 'iNeuron15923026', 'correct sample id');
+  is ($sample->library_name(), '1_GEX_iA_iN_SCREEN', 'correct library name');
+  is ($sample->index_label(), 'Z0001', 'correct index label');
+  is ($sample->index_sequence(), 'CAGCTCGAATGCGAT', 'correct index sequence');
+  is ($sample->tag_index, 1, 'correct NPG tag index');
+}
+is ($samples_li->[0]->application_type(), 'scRNA_GEX_10x_5prime_v3',
+  'correct application type');
+is ($samples_ma->[0]->application_type(), undef, 'undefined application type');
 
-is (scalar @{$samples_from_li}, 8, 'returned eight samples');
-is_deeply ($samples_from_li, $samples_from_ma, 'identical sample info');
-my $sample = $samples_from_li->[0];
-is ($sample->id(), 'iNeuron15923026', 'correct sample id');
-is ($sample->library_name(), '1_GEX_iA_iN_SCREEN', 'correct library name');
-is ($sample->index_label(), 'Z0001', 'correct index label');
-is ($sample->index_sequence(), 'CAGCTCGAATGCGAT', 'correct index sequence');
-is ($sample->tag_index, 1, 'correct NPG tag index');
+for my $sample (($samples_li->[7], $samples_ma->[7])) {
+  is ($sample->id(), 'iNeuron15923033', 'correct sample id');
+  is ($sample->library_name(), '4_dgRNA_iA_iN_SCREEN', 'correct library name');
+  is ($sample->index_label(), 'Z0008', 'correct index label');
+  is ($sample->index_sequence(), 'CACATCCTGCATGTGAT', 'correct index sequence');
+  is ($sample->tag_index, 8, 'correct NPG tag index');
+}
+is ($samples_li->[7]->application_type(), 'native',
+  'correct application type');
+is ($samples_ma->[7]->application_type(), undef, 'undefined application type');
 
 1;

t/data/ultimagen/425347-20250821_1214/425347_LibraryInfo.xml

@@ -43,8 +43,8 @@
     <Sample Id="iNeuron15923033@4_dgRNA_iA_iN_SCREEN" Index_Label="Z0008" Index_Sequence="CACATCCTGCATGTGAT">
       <Attribute Name="Barcode_Plate_Num" Value="1" />
       <Attribute Name="Barcode_Plate_Well" Value="H1" />
-      <Attribute Name="application_type" Value="scRNA_CRISPR_10x_5prime_v3" />
+      <Attribute Name="application_type" Value="native" />
     </Sample>
   </Samples>
   <Sequencing />
-  <Analysis_Recipe Name="Other" />18Aug25 D7_CooperSteer_5priem plus guide</SampleInfo>
+  <Analysis_Recipe Name="Other" />18Aug25 D7_CooperSteer_5priem plus guide</SampleInfo>