Merge pull request #796 from mgcam/daemon4novaseqx_samplesheet

Daemon4novaseqx samplesheet

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

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

@@ -65,8 +65,8 @@ npg_samplesheet_generator_NovaSeqXSeries
 
 =head1 DESCRIPTION
 
-Generates a samplesheet for the NovaSeq Series X Illumina instrument and
-DRAGEN analysis.
+Generates a single samplesheet for the NovaSeq Series X Illumina instrument
+and DRAGEN analysis.
 
 =head1 EXIT STATUS
 

lib/npg/samplesheet.pm

@@ -60,24 +60,6 @@ Readonly::Scalar my $MIN_COLUMN_NUM => 3;
 ####################### Public attributes ########################
 ##################################################################
 
-=head2 id_run
-
-An optional attribute
-
-=cut
-
-has '+id_run' => (
-  'lazy_build' => 1,
-  'required'   => 0,
-);
-sub _build_id_run {
-  my ($self) = @_;
-  if($self->has_tracking_run()){
-    return $self->run()->id_run();
-  }
-  croak 'id_run or a run is required';
-}
-
 =head2 extend
 
 A boolean attribute, false by default.
@@ -509,7 +491,7 @@ David K. Jackson E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2019, 2020, 2023 Genome Research Ltd.
+Copyright (C) 2019,2020,2023,2024 Genome Research Ltd.
 
 This file is part of NPG.
 

lib/npg/samplesheet/auto.pm

@@ -8,18 +8,24 @@ use Readonly;
 use File::Copy;
 use File::Spec::Functions;
 use Carp;
+use List::MoreUtils qw(none);
 
-use npg::samplesheet;
 use npg_tracking::Schema;
 use WTSI::DNAP::Warehouse::Schema;
 use st::api::lims::samplesheet;
+use npg::samplesheet;
+use npg::samplesheet::novaseq_xseries;
 
 with q(MooseX::Log::Log4perl);
 
 our $VERSION = '0';
 
 Readonly::Scalar my $MISEQ_INSTRUMENT_FORMAT => 'MiSeq';
 Readonly::Scalar my $DEFAULT_SLEEP => 90;
+Readonly::Array my @INSTRUMENT_FORMATS => (
+  $MISEQ_INSTRUMENT_FORMAT,
+  $npg::samplesheet::novaseq_xseries::NX_INSTRUMENT_FORMAT
+);
 
 ##no critic (Subroutines::ProhibitUnusedPrivateSubroutine)
 
@@ -97,7 +103,7 @@ Tests that a valid instrument format is used.
 
 sub BUILD {
   my $self = shift;
-  if ($self->instrument_format ne $MISEQ_INSTRUMENT_FORMAT) {
+  if (none {$self->instrument_format eq $_ } @INSTRUMENT_FORMATS) {
     my $m = sprintf
       'Samplesheet auto-generator is not implemented for %s instrument format',
       $self->instrument_format;
@@ -141,9 +147,20 @@ sub process {
     my $id_run = $r->id_run;
     $self->log->info('Considering ' . join q[,],$id_run,$r->instrument->name);
 
-    my $ss = npg::samplesheet->new(
-      run => $r, mlwh_schema => $self->mlwh_schema
-    );
+    my $ss;
+    if ($self->instrument_format eq $MISEQ_INSTRUMENT_FORMAT) {
+      $ss = npg::samplesheet->new(
+        run => $r,
+        mlwh_schema => $self->mlwh_schema
+      );
+    } else {
+      $ss = npg::samplesheet::novaseq_xseries->new(
+        run => $r,
+        mlwh_schema => $self->mlwh_schema,
+        align => 1
+      );
+    }
+
     my $method_name =
       '_valid_samplesheet_file_exists_for_' . $self->instrument_format;
     my $generate_new = !$self->$method_name($ss, $id_run);
@@ -241,6 +258,22 @@ sub _valid_samplesheet_file_exists_for_MiSeq {##no critic (NamingConventions::Ca
   return;
 }
 
+sub _valid_samplesheet_file_exists_for_NovaSeqX {##no critic (NamingConventions::Capitalization)
+  my ($self, $ss_object, $id_run) = @_;
+
+  # The default samplesheet name starts with the date string. A new
+  # samplesheet will be generated each day. Not a problem since the run
+  # should either progress or be cancelled. 
+
+  my $o = $ss_object->output;
+  if (-e $o) {
+    $self->log->info(qq($o already exists for $id_run));
+    return 1;
+  };
+
+  return;
+}
+
 __PACKAGE__->meta->make_immutable;
 
 1;
@@ -273,6 +306,8 @@ __END__
 
 =item Carp
 
+=item List::MoreUtils
+
 =item npg_tracking::Schema
 
 =item npg::samplesheet
@@ -293,7 +328,7 @@ David K. Jackson E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2012,2013,2014,2019,2021,2023 GRL.
+Copyright (C) 2012,2013,2014,2019,2021,2023,2024 GRL.
 
 This file is part of NPG.
 

lib/npg/samplesheet/base.pm

@@ -57,8 +57,16 @@ Run ID, an optional attribute.
 =cut
 
 has '+id_run' => (
+  'lazy_build' => 1,
   'required'   => 0,
 );
+sub _build_id_run {
+  my $self = shift;
+  if ($self->has_tracking_run()) {
+    return $self->run()->id_run();
+  }
+  croak 'id_run or a run is required';
+}
 
 
 =head2 batch_id
@@ -228,7 +236,7 @@ Marina Gourtovaia E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2019, 2020, 2023 Genome Research Ltd.
+Copyright (C) 2019,2020,2023,2024 Genome Research Ltd.
 
 This file is part of NPG.
 

lib/npg/samplesheet/novaseq_xseries.pm

@@ -10,14 +10,18 @@ use List::MoreUtils qw(any none uniq);
 use List::Util qw(first max);
 use DateTime;
 use Data::UUID;
+use Try::Tiny;
 
+use npg_tracking::util::types;
 use st::api::lims::samplesheet;
 
 extends 'npg::samplesheet::base';
 with    'MooseX::Getopt';
 
 our $VERSION = '0';
 
+Readonly::Scalar our $NX_INSTRUMENT_FORMAT => 'NovaSeqX';
+
 Readonly::Scalar my $READ1_LENGTH => 151;
 Readonly::Scalar my $READ2_LENGTH => 151;
 Readonly::Scalar my $LIST_INDEX_TAG1  => 2;
@@ -98,7 +102,7 @@ has 'dragen_software_version' => (
 sub _build_dragen_software_version {
   my $self = shift;
 
-  if (!$self->has_id_run) {
+  if (!$self->id_run) {
     croak 'DRAGEN software version cannot be retrieved. ' .
       'Either supply it as an argument or supply existing id_run';
   }
@@ -135,7 +139,7 @@ sub _build_file_name {
   my $self = shift;
 
   my $file_name;
-  if ($self->has_id_run) {
+  if ($self->id_run) {
     $file_name = join q[_],
       $self->run_name,
       q[ssbatch] . $self->batch_id;
@@ -185,10 +189,24 @@ sub _build_output {
 
 
 has '+id_run' => (
+  'isa'           => 'Maybe[NpgTrackingRunId]',
   'documentation' => 'NPG run ID, optional; if supplied, the record for this '.
                      'run should exists in the run tracking database',
 );
+around '_build_id_run' => sub {
+  my $orig = shift;
+  my $self = shift;
 
+  # Parent's builder method errors if id_run cannot be inferred from
+  # the database record. Here we allow for this attribute to be undefined.
+  # Depending on how other atributes are defined, it might be possible to
+  # generate the samplesheet.
+  my $id_run;
+  try {
+    $id_run = $self->$orig(@_);
+  };
+  return $id_run;
+};
 
 has '+batch_id' => (
   'documentation' => 'LIMS batch identifier, optional. If not set, will be ' .
@@ -325,7 +343,7 @@ sub _build_run_name {
 
   my $run_name;
   if ($self->id_run()) {
-    if ($self->run->instrument_format()->model() !~ /NovaSeqX/smx) {
+    if ($self->run->instrument_format()->model() !~ /$NX_INSTRUMENT_FORMAT/smx) {
       croak 'Instrument is not registered as NovaSeq X Series ' .
             'in the tracking database';
     }
@@ -865,6 +883,10 @@ __END__
 
 =item Data::UUID
 
+=item Try::Tiny
+ 
+=item npg_tracking::util::types
+
 =back
 
 =head1 BUGS AND LIMITATIONS
@@ -877,7 +899,7 @@ Marina Gourtovaia E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2023 Genome Research Ltd.
+Copyright (C) 2023,2024 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