Fixed a bug in the autoqc function package.

The runfolder_path attribute is passed to the constructor
of the review autoqc check object when deciding whether
this check should run.

Updated the RoboQC section of the existing test product
configuration file.

Changes

@@ -9,7 +9,8 @@ LIST OF CHANGES
    the checksum of the downloaded script to the expected value. We now store
    an updated expected checksum value, which corresponds to the latest release.
  - GitHub CI - updated deprecated v2 runner to v3
-
+ - The runfolder_path attribute is passed to the constructor of the review
+   autoqc check object when deciding whether this check should run.
 
 release 68.5.0 (2024-09-04)
  - The runfolder_path argument is added to the command for the autoqc review

MANIFEST

@@ -1041,6 +1041,7 @@ t/data/release/config/haplotype_caller_on_study_specific_reference/product_relea
 t/data/release/config/notify_off/product_release.yml
 t/data/release/config/notify_on/product_release.yml
 t/data/release/config/qc_review/product_release.yml
+t/data/release/config/qc_review_default/product_release.yml
 t/data/release/config/pp_archival/product_release.yml
 t/data/release/config/pp_archival/product_release_no_array.yml
 t/data/release/config/pp_archival/product_release_no_filters.yml

lib/npg_pipeline/function/autoqc.pm

@@ -318,6 +318,7 @@ sub _should_run {
       $init_hash{'is_paired_read'} = $self->is_paired_read() ? 1 : 0;
     } elsif ($self->qc_to_run() eq 'review') {
       $init_hash{'product_conf_file_path'} = $self->product_conf_file_path;
+      $init_hash{'runfolder_path'} = $self->runfolder_path;
     } elsif ($self->qc_to_run() eq 'genotype') {
       my $ref_fasta = npg_pipeline::cache::reference->instance()
 	              ->get_path($product, q(fasta), $self->repository());
@@ -416,7 +417,7 @@ Marina Gourtovaia
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2018,2019,2020 Genome Research Ltd.
+Copyright (C) 2018,2019,2020,2024 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-autoqc.t

@@ -40,6 +40,8 @@ my $archive_dir = $hiseq_rf->{'archive_path'};
 my $rf_path     = $hiseq_rf->{'runfolder_path'};
 fcopy('t/data/run_params/runParameters.hiseq.xml', "$rf_path/runParameters.xml")
   or die 'Fail to copy run param file';
+fcopy('t/data/run_params/RunInfo.hiseq.rr.xml',  "$rf_path/RunInfo.xml")
+  or die 'Fail to copy run info file';
 
 my $default = {
   default => {
@@ -574,7 +576,7 @@ subtest 'genotype and gc_fraction and bcfstats' => sub {
 };
 
 subtest 'review' => sub {
-  plan tests => 6;
+  plan tests => 8;
 
   local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet_8747.csv';
 
@@ -625,6 +627,23 @@ subtest 'review' => sub {
     qq{--qc_in=$archive_dir/lane1/plex1/qc --conf_path=t/data/release/config/qc_review } .
     qq{--runfolder_path=$rf_path};
   is ($d->command, $expected_command, 'correct command for plex-level job');
+
+  $qc = npg_pipeline::function::autoqc->new(
+    qc_to_run         => 'review',
+    is_indexed        => 1,
+    id_run            => 8747,
+    runfolder_path    => $rf_path,
+    timestamp         => q{today},
+    conf_path         => q{t/data/release/config/qc_review_default},
+    resource          => $default
+  );
+
+  $da = $qc->create();
+  ok ($da && (@{$da} == 6), '6 definitions returned');
+  %definitions = map { $_->composition->freeze2rpt => $_ } @{$da};
+  @expected_rpt_lists = map { "8747:$_:168"} qw/1 2 3 4 5 6/;
+  is_deeply ([sort keys %definitions], \@expected_rpt_lists,
+    'definitions are for correct entities');
 };
 
 subtest 'interop' => sub {

t/data/release/config/qc_review/product_release.yml

@@ -5,19 +5,21 @@ default:
 study:
   - study_id: "1713"
     robo_qc:
+      qc_type: "mqc"
       criteria:
         - applicability_criteria:
-          lims:
-            - library_type:
-              - "Agilent Pulldown"
+            lims:
+              library_type:
+                - "Agilent Pulldown"
           acceptance_criteria:
             - "criteria1"
   - study_id: "2410"
     robo_qc:
+      qc_type: "mqc"
       criteria:
         - applicability_criteria:
-          lims:
-            - library_type:
-              - "Custom"
+            lims:
+              library_type:
+                - "Custom"
           acceptance_criteria:
             - "criteria2"

t/data/release/config/qc_review_default/product_release.yml

@@ -0,0 +1,22 @@
+---
+common:
+  irods: &no_irods
+    enable: false
+default:
+  irods: &default_irods
+    enable: true
+  data_deletion:
+    staging_deletion_delay: 30
+  markdup_method: "biobambam"
+  gbs_pipeline: &gbs_pipeline_accessible
+    allowed: true
+  robo_qc:
+    qc_type: "mqc"
+    criteria:
+      - applicability_criteria:
+          lims:
+            is_control: 1
+          sequencing_run:
+            platform_HiSeq: 1
+        acceptance_criteria:
+          - "sequence_error.pass"