Throwaway

.github/workflows/run-tests.yml

@@ -13,9 +13,9 @@ jobs:
     env:
       PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
       NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
-      WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
-      WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF}
-
+      WSI_NPG_GITHUB_URL: https://github.com/jmtcsngr
+      WSI_NPG_BUILD_BRANCH: ${{ github.base_ref}}
+      WSI_NPG_GITHUB_REPO_OWNER: ${{ github.repository_owner }}
 
     strategy:
       matrix:

Build.PL

@@ -121,7 +121,6 @@ my $builder = $class->new(
                 'base'                            => '2.12',
                 'Carp'                            => '1.04',
                 'CGI'                             => '3.52',
-                'Class::Accessor'                 => '0.31',
                 'Class::Load'                     => 0,
                 'Class::Std'                      => '0.0.8',
                 'ClearPress'                      => '>= 473.3.3',

Changes

@@ -1,5 +1,79 @@
 LIST OF CHANGES
 
+ - st::api::lims
+     - Removed batch_id constructor argument. It was used by the xml driver,
+       it is no longer required.
+     - Fix a bug in propagating driver details to children to ensure that
+       (1) a switch of the driver type does not happen;
+       (2) the database handle and the flowcell ID are passed to children
+           consistently.
+ - Removed provisions for the xml st::api::lims driver from the old samplesheet
+   generator npg::samplesheet.
+ - To avoid code repetitions, created a parent class for different samplesheet
+   generators and moved common code there.
+ - Extended the code for the samplesheet daemon to generate samplesheets for
+   NovaSeqX instruments.
+ - Removed remaining unused test data from the era of xml st::api::lims driver.
+ - Updated signature and iRODS documentation link in template for emails
+ - Updated NPG tracking url to https protocol and port for links in emails
+ - Removed link to illumina/runs qc page in emails reporting status change event
+   to subscribers
+
+release 98.1.0
+ - Added a new method, latest_revision_for_modification, to
+   npg_tracking::Schema::Result::Instrument to retrieve the latest modification
+   revision for the instrument.
+ - Added 'dragen_software_version' script argument
+   for bin/npg_samplesheet_generator_NovaSeqXSeries. If not set and
+   id_run is defined, defaults to the record for the latest 'Dragen'
+   modification for the NovaSeqX instrument on which the flowcell will be
+   sequenced.
+
+release 98.0.0
+ - Removed the use of 'xml' lims driver from all tests.
+ - Deleted 'xml' lims driver class and all classes which supported this
+   functionality, together with all related tests and test data.
+ - In release 97.0.0, the default LIMS driver type in samplesheet generation
+   was changed to 'ml_warehouse'. Following this change, the code for
+   auto-generation of MiSeq default samplesheets is now simplified to exclude
+   an explicit creation of LIMS objects.
+ - Changes to st::api::lims, which are not related to the 'xml' lims driver
+   removal:
+     - deleted all previously deprecated methods ('seq_qc_state',
+       'associated_lims', 'associated_child_lims', 'associated_child_lims_ia');
+     - deleted methods for which we do not have data in ml warehouse, our
+       primary source of LIMS data ('request_id', 'project_id', 'project_name');
+     - deleted all code for computing inline tag indexes and inferring
+       tag sequences and library types from sample description since
+       definitions like this have not been in use for the last six years;
+     - reimplemented the 'reference_genome' method to exclude a fallback to
+       a study reference for tag zero and lane-level objects when samples
+       have different references;
+     - ensured 'required_insert_size' method works correctly for objects that
+       are initialised with the 'rpt_list' attribute, ie have the 'position'
+       attribute undefined;
+     - added 'aggregate_libraries' method, which is similar to the existing
+       'aggregate_xlanes' method, but instead of getting an instruction to
+       merge libraries, discovers the libraries which can be merged and returns
+       a list of merged entities and, separately, a list of singletons.
+ - npg_tracking::illumina::run::long_info role:
+     - restricted the 'all_lanes_mergeable' flag to NovaSeq Standard workflow,
+       ie dropped an additional case of HiSeq Rapid Run since HiSeq instruments
+       are no longer in use;
+     - ensured the detection of NovaSeqX and NovaSeq instrument types is
+       unambiguous.
+ - Updated DBIx classes from the prod database. Changes are due to the MySQL
+   database server upgrade to v8.+
+ - Finding the runfolder path - stopped errors being raised when a runfolder
+   is found in 'analysis' or 'outgoing' in the presence of a duplicate runfolder
+   in 'incoming' (the duplicates in 'incoming' are sometimes created by
+   instruments well after the run was mirrored and the runfolder moved to
+   'analysis'). The duplicate runfolder in 'incoming' is disregarded'.
+ - DRAGEN samplesheet generation - limit analysis to human samples only.
+ - Fixed incorrect string comparison in the npg_move_runfolder script.
+ - Ensure that pull requests to the master branch source dependencies from
+   master branches (devel branch was hardcoded).
+
 release 97.0.2
  - pin DBD::mysql to 4.050 to keep temp support for old mysql clients