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/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 +147,21 @@ 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(
+        id_run => $id_run,
+        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 +259,22 @@ 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;

lib/npg/samplesheet/novaseq_xseries.pm

@@ -18,6 +18,8 @@ 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;
@@ -325,7 +327,7 @@ 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';
     }

t/47-npg_samplesheet_auto.t

@@ -1,17 +1,21 @@
 use strict;
 use warnings;
-use Test::More tests => 12;
+use Test::More tests => 15;
 use Test::Exception;
 use File::Temp qw/ tempdir /;
 use Moose::Meta::Class;
 use Log::Log4perl qw(:easy);
+use File::chdir;
+use Perl6::Slurp;
 
 use_ok('npg::samplesheet::auto');
 
 my $util = Moose::Meta::Class->create_anon_class(
              roles => [qw/npg_testing::db/])->new_object({});
-my $schema_wh = $util->create_test_db(q[WTSI::DNAP::Warehouse::Schema]);
-my $schema = $util->create_test_db(q[npg_tracking::Schema]);
+my $schema_wh = $util->create_test_db(q[WTSI::DNAP::Warehouse::Schema],
+                                      q[t/data/fixtures_lims_wh]);
+my $schema = $util->create_test_db(q[npg_tracking::Schema],
+                                   q[t/data/dbic_fixtures]);
 
 {
   my $sm;
@@ -27,15 +31,15 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema]);
     instrument_format   => 'NovaSeq'
   )}
   qr/Samplesheet auto-generator is not implemented for NovaSeq instrument format/,
-  'MiSeq error for an invalid instrument format';
+  'Error for an invalid instrument format';
 }
 
 {
   is(npg::samplesheet::auto::_id_run_from_samplesheet(
       't/data/samplesheet/miseq_default.csv'), 10262,
       'id run retrieved from a samplesheet');
   lives_and { is npg::samplesheet::auto::_id_run_from_samplesheet('some_file'), undef}
-      'undef reftuned for a non-exisitng samplesheet';
+      'undef returned for a non-exisitng samplesheet';
 }
 
 {
@@ -66,4 +70,33 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema]);
   ok(-e $new_file, 'moved file is in samplesheet_old directory');
 }
 
+{
+  my $dir = tempdir(UNLINK => 1);
+  mkdir "$dir/samplesheets";
+
+  my $id_run = 47995;
+  my $run_row = $schema->resultset('Run')->find($id_run);
+  $run_row->update_run_status('run pending');
+  is ($run_row->current_run_status_description(), 'run pending',
+    "run $id_run should be picked up by the daemon");
+  {
+    local $CWD = $dir;
+    diag `ls -l`;
+    npg::samplesheet::auto->new(
+      npg_tracking_schema => $schema,
+      mlwh_schema         => $schema_wh,
+      instrument_format   => 'NovaSeqX'
+    )->process();
+  }
+  my $glob = q[*_47995_NVX1_A_ssbatch98292.csv];
+  my @files = glob "$dir/samplesheets/$glob";
+  is (@files, 1, 'one NovaSeqX samplesheet file is generated');
+  my $compare_file = 't/data/samplesheet/dragen/' .
+                     '231206_47995_NVX1_A_ssbatch98292_align.csv';
+  my $expected = slurp($compare_file);
+  $expected =~ s/KeepFastq,TRUE,,,/KeepFastq,FALSE,,,/;
+  is (slurp($files[0]), $expected,
+    'the NovaSeqX samplesheet is generated correctly');
+}
+
 1;