Merge branch 'devel' into GBSac

Build.PL

@@ -86,7 +86,6 @@ my $builder = $class->new(
           'npg_tracking::glossary::rpt'                        => 0,
           'npg_tracking::glossary::composition::factory::rpt_list' => 0,
           'npg_tracking::illumina::runfolder'                  => 0,
-          'npg_tracking::illumina::run::folder::validation'    => 0,
           'npg_tracking::Schema'                               => 0,
           'npg_tracking::util::types'                          => 0,
           'npg_tracking::util::abs_path'                       => 0,

Changes

@@ -5,6 +5,36 @@ LIST OF CHANGES
  - allow samtools ampliconclip to run for GBS products where primer panel
    has primer bed file in the repository
 
+release 68.0.0
+ - Use st::api::lims->aggregate_libraries() method for both 'merge_lanes' and
+   'merge_by_library' pipeline options. This is a breaking change as far as
+   archival and deletion of NovaSeq Standard workflow data is concerned.
+   Key change for lane merging for this data will be that tag 0 and tag 888 will
+   not be merged across the lanes.
+   The NovaSeq Standard workflow, where there is only one input port, is
+   different to the more general merging across lanes where the (claimed) same
+   library has been sequenced. But this is not a valid reason to maintain separate
+   code.
+ - Deletable shadow folders are detected, but not considered as deletable
+   for now. They are flagged in the log of the 'npg_run_is_deletable' script.
+ - Removed all code that was used for the UKB project and the upload of Heron
+   project data to CLIMB. Updated the archival pipeline function graph and its
+   graphical representation.
+    - Removed 'cache_merge_component' and 'archive_to_s3' pipeline functions.
+    - Removed all functions for retrieving the QC state of the product
+      from 'npg_pipeline::product'.
+    - Dropped npg_pipeline::base dependency on QC database ('qc_schema'
+      attribute for 'npg_qc::Schema'). Removed test fixtures for the QC database.
+    - Deleted 'npg_receipt4run_is_deletable' script.
+    - Dropped checks for files upload to the third-party cloud locations when
+      deciding whether the run folder is deletable.
+    - Updated examples in POD in 'npg_pipeline::product::release'.
+    - Excluded redundant settings from 'product_release.yml' files used in
+      unit tests.
+
+release 67.1.1
+ - Fixed correct pp collection root for MiSeq
+
 release 67.1.0
  - Fix typo in analysis specific overrides for bwa_als_se mapping to bwa0_6
  - Add in use of autosome target regions for BGE libraries in seq_alignment

bin/npg_run_is_deletable

@@ -19,7 +19,6 @@ my $their_log_level = $verbose ? 'DEBUG' : 'WARN';
 ##no critic (ValuesAndExpressions::ProhibitImplicitNewlines)
 my $log4perl_config = qq(
   log4perl.logger                                  = $my_log_level, A1
-  log4perl.category.npg_pipeline.validation.s3     = $their_log_level, A1
   log4perl.category.npg_pipeline.validation.irods  = $their_log_level, A1
   log4perl.category.npg_pipeline.validation.autoqc = $their_log_level, A1
   log4perl.logger.WTSI.NPG.iRODS                   = OFF, A1