Merge pull request wtsi-npg#783 from mgcam/dragen_no_delete

Runs with data analysed on-board are not deletable.
dkj · Jul 11, 2023 · 8e44aab · 8e44aab
2 parents 0448b10 + 5961d9c
commit 8e44aab
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Showing 3 changed files with 34 additions and 3 deletions.
diff --git a/.github/workflows/testing_and_building_repo.yml b/.github/workflows/testing_and_building_repo.yml
@@ -1,5 +1,7 @@
 name: testing_and_building_repo
 on: [push, pull_request]
+env:
+  WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -50,7 +52,6 @@ jobs:
           ${GITHUB_WORKSPACE}/scripts/install_npg_perl_dependencies.sh $WTSI_NPG_GITHUB_URL $WTSI_NPG_BUILD_BRANCH
       env:
         WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
-        WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF} #getting name of current github branch
 
     - name: Install cpanm dependencies
       run: |

diff --git a/lib/npg_pipeline/validation.pm b/lib/npg_pipeline/validation.pm
@@ -468,6 +468,7 @@ sub run {
               $self->_lims_deletable()         &&
               $self->_staging_deletable()      &&
               $self->_irods_seq_deletable()    &&
+              $self->_irods_seq_onboard_deletable() &&
               $self->_s3_deletable()           &&
               $self->_autoqc_deletable()       &&
               $self->_file_archive_deletable
@@ -831,6 +832,11 @@ sub _irods_seq_pp_deletable {
   return $deletable;
 }
 
+sub _irods_seq_onboard_deletable {
+  my $self = shift;
+  return !$self->onboard_analysis_planned();
+}
+
 sub _irods_destination_collection4pp {
   my $self = shift;
 
@@ -1109,7 +1115,7 @@ __END__
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2019,2020,2021,2022 Genome Research Ltd.
+Copyright (C) 2019,2020,2021,2022,2023 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

diff --git a/t/10-validation.t b/t/10-validation.t
@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 7;
+use Test::More tests => 8;
 use Test::Exception;
 use Test::Warn;
 use Test::Trap qw/ :warn /;
@@ -334,4 +334,28 @@ subtest 'per product flag and iRODS locations' => sub {
     'iRODS collection as set');
 };
 
+subtest 'presence of onboard analysis results' => sub {
+  plan tests => 2;
+
+  my $rf_path = tempdir(CLEANUP => 1);
+
+  copy('t/data/run_params/RunParameters.novaseqx.xml',
+    "$rf_path/RunParameters.xml");
+  my $v = npg_pipeline::validation->new(
+    id_run => 47539,
+    runfolder_path => $rf_path
+  );
+  ok (!$v->_irods_seq_onboard_deletable(),
+    'NovaSeqX with onboard analysis - not deletable');
+
+  copy('t/data/run_params/runParameters.novaseq.xml',
+    "$rf_path/RunParameters.xml"); 
+  $v = npg_pipeline::validation->new(
+    id_run => 9999,
+    runfolder_path => $rf_path
+  );
+  ok ($v->_irods_seq_onboard_deletable(),
+    'NovaSeq - no onboard analysis - deletable');
+};
+
 1;