pull from devel to master to create release 99.0.0

.github/workflows/run-tests.yml

@@ -14,8 +14,8 @@ jobs:
       PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
       NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
       WSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
-      WSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
-
+      WSI_NPG_BUILD_BRANCH: ${{ github.base_ref}}
+      WSI_NPG_GITHUB_REPO_OWNER: ${{ github.repository_owner }}
 
     strategy:
       matrix:

Changes

@@ -1,5 +1,25 @@
 LIST OF CHANGES
 
+release 99.0.0
+ - 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

MANIFEST

@@ -3,6 +3,8 @@ bin/illumina_instruments_uptime
 bin/npg_daemon_control
 bin/npg_move_runfolder
 bin/npg_samplesheet4MiSeq
+bin/npg_samplesheet4NovaSeqX
+bin/npg_samplesheet_generator_NovaSeqXSeries
 bin/npg_status_save
 bin/staging_area_monitor
 bin/npg_deletable_dr_runs
@@ -161,6 +163,7 @@ lib/npg_tracking/report/event2followers.pm
 lib/npg_tracking/report/event2subscribers.pm
 lib/npg_tracking/report/events.pm
 lib/npg/samplesheet.pm
+lib/npg/samplesheet/base.pm
 lib/npg/samplesheet/novaseq_xseries.pm
 lib/npg/samplesheet/auto.pm
 lib/npg/util.pm
@@ -687,6 +690,9 @@ t/data/samplesheet/miseq_extended.csv
 t/data/samplesheet/multilane.csv
 t/data/samplesheet/novaseq_multirun.csv
 t/data/samplesheet/samplesheet_47539.csv
+t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292.csv
+t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_align.csv
+t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_varcall.csv
 t/data/test40_lims/samplesheet_novaseq4lanes.csv
 t/data/test40_lims/samplesheet_rapidrun_nopool.csv
 t/data/test_staging_daemon/novaseqxplus/RunInfo.xml

bin/npg_samplesheet4MiSeq

@@ -13,7 +13,7 @@ our $VERSION = '0';
 Log::Log4perl->easy_init($INFO);
 
 my $log = Log::Log4perl->get_logger('main');
-$log->info('Starting npg samplesheet');
+$log->info('Starting npg samplesheet daemon for MiSeq instruments');
 
 npg::samplesheet::auto->new()->loop();
 

bin/npg_samplesheet4NovaSeqX

@@ -0,0 +1,98 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" );
+use Log::Log4perl qw(:easy);
+
+use npg::samplesheet::auto;
+
+our $VERSION = '0';
+
+Log::Log4perl->easy_init($INFO);
+
+my $log = Log::Log4perl->get_logger('main');
+$log->info('Starting npg samplesheet daemon for NovaSeqX instruments');
+
+npg::samplesheet::auto->new(instrument_format => 'NovaSeqX')->loop();
+
+0;
+
+__END__
+
+=head1 NAME
+
+npg_samplesheet4NovaSeqX
+
+=head1 USAGE
+
+  npg_samplesheet4NovaSeqX
+
+=head1 DESCRIPTION
+
+The script, once started, runs in perpetuity, generating Illumina-style
+samplesheets for any NovaSeqX run with status 'run pending'.
+
+=head1 REQUIRED ARGUMENTS
+
+None
+
+=head1 OPTIONS
+
+=head1 DIAGNOSTICS
+
+=head1 CONFIGURATION
+
+Access to both npg_tracking and ml warehouse database is required.
+
+=head1 DEPENDENCIES
+
+=over
+
+=item strict
+
+=item warnings
+
+=item FindBin
+
+=item lib
+
+=item Log::Log4perl
+
+=item npg::samplesheet::auto
+
+=back
+
+=head1 EXIT STATUS
+
+  Does not exit unless is sent a signal to terminate.
+
+=head1 INCOMPATIBILITIES
+
+=head1 BUGS AND LIMITATIONS
+
+=head1 AUTHOR
+
+Marina Gourtovaia E<lt>[email protected]<gt>
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright (C) 2023 GRL.
+
+This file is part of NPG.
+
+NPG is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+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

bin/npg_samplesheet_generator_NovaSeqXSeries

@@ -27,26 +27,46 @@ npg_samplesheet_generator_NovaSeqXSeries
 
   C<help>     - displays help message and exists
 
-  C<varcall>  - variant calling mode, defaults to C<None>, other valid options
-                C<SmallVariantCaller> and C<AllVariantCallers>
 
   C<batch_id> - LIMS batch identifier, optional
 
   C<id_run>   - NPG run ID, optional; if supplied, the record for this run
                 should exists in the run tracking database
+
+  C<read_length> -
+                an optional list of read lengths, forward first, reverse
+                second; currently both default to 151
+
+  C<index_read_length> -
+                an optional list of index read lengths for the first and,
+                optionally, second index read; if not given, computed from
+                the length of barcodes recorded in LIMS
+
   C<align>    - a boolean option, false by default; if set, the DRAGEN
                 germline analysis section is added to the file if suitable
                 samples are present
-  C<keep_fastq> - an option to keep FASTQ files for aligned data, false
-                  default
-  C<dragen_max_number_of_configs> - DRAGEN analysis can deal with a limited
-                  number of distinct configurations. Set this attribute if
-                  processing not on-board.
+
+  C<varcall>  - variant calling mode, defaults to C<None>, other valid options
+                C<SmallVariantCaller> and C<AllVariantCallers>
+
+  C<keep_fastq> -
+                an option to keep FASTQ files for aligned data, false by
+                default
+
+  C<dragen_max_number_of_configs> -
+                DRAGEN analysis can deal with a limited number of distinct
+                configurations. Set this attribute if processing off-board.
+
+  C<dragen_software_version> -
+                DRAGEN software version to use, optional
+
+  C<file_name> -
+                name of the samplesheet CSV file, optional
 
 =head1 DESCRIPTION
 
-Samplesheet generation to initiate DRAGEN analysis of data sequenced
-on the NovaSeq Series X Illumina instrument.
+Generates a single samplesheet for the NovaSeq Series X Illumina instrument
+and DRAGEN analysis.
 
 =head1 EXIT STATUS
 
@@ -56,37 +76,13 @@ on the NovaSeq Series X Illumina instrument.
 
 =head1 CONFIGURATION
 
-Access to the ml warehouse database is required.
+Access to both ml warehouse and npg tracking  database is required.
 
 =head1 DEPENDENCIES
 
 =over
 
-=item strict
-
-=item warnings
-
-=item Carp
-
-=item Text::CSV
-
-=item Readonly
-
-=item List::MoreUtils
-
-=item List::Util
-
-=item Getopt::Long
-
-=item Pod::Usage
-
-=item DateTime
-
-=item Data::UUID
-
-=item st::api::lims
-
-=item npg_tracking::Schema
+=item npg::samplesheet::novaseq_xseries
 
 =back
 

data/npg_tracking_email/templates/run_status2followers.tt2

@@ -11,13 +11,12 @@ Study '[% lanes.0.study_name %]' has samples in the following lanes of this run:
 Sequencing and default analysis for this run completed. Run is now pending manual QC review. Meanwhile, we will be loading analysis results into iRODS.
 [%- END %]
 [%- IF status_description == 'qc complete' -%]
-The manual QC review is complete and your data should now be available from iRODS (see http://scratchy.internal.sanger.ac.uk/wiki/index.php/IRODS_for_Sequencing_Users ). 
+The manual QC review is complete and your data should now be available from iRODS (see https://ssg-confluence.internal.sanger.ac.uk/display/FARM/iRODS ).
 [%- END %]
 
 NPG page for the run:
 [% PROCESS urls.tt2 %][% npg_tracking_url %]/run/[% id_run %]
 
 Analysis and QC information for this run will be/is available:
-[% seqqc_url %]/illumina/runs/[% id_run %]
 [% seqqc_url %]/checks/runs/[% id_run %]
 [% END %]

data/npg_tracking_email/templates/urls.tt2

@@ -1,4 +1,4 @@
 [%
   seqqc_url = 'http://sfweb.internal.sanger.ac.uk:1959';
-  npg_tracking_url = 'http://sfweb.internal.sanger.ac.uk:9000/perl/npg';
+  npg_tracking_url = 'https://sfweb.internal.sanger.ac.uk:12443/perl/npg';
 %]

data/npg_tracking_email/templates/wrapper.tt2

@@ -1,2 +1,2 @@
 [% content %]
-NPG, DNA Pipelines Informatics
+NPG on behalf of DNA Pipelines and GSLP