From c96f724ac92cbc01a589bdf379a469ed9486ee68 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 4 Dec 2023 11:55:42 +0000 Subject: [PATCH 01/28] Updated branch for dependencies on push. --- .github/workflows/run-tests.yml | 4 ++-- scripts/install_wsi_dependencies.sh | 11 ++++++++++- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index e18cba94..5e76c9ab 100644 --- a/.github/workflows/run-tests.yml +++ b/.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: ${{ github.repository_owner }} strategy: matrix: diff --git a/scripts/install_wsi_dependencies.sh b/scripts/install_wsi_dependencies.sh index 975a3c15..78a20967 100755 --- a/scripts/install_wsi_dependencies.sh +++ b/scripts/install_wsi_dependencies.sh @@ -3,7 +3,16 @@ set -e -u -x WSI_NPG_GITHUB_URL=${WSI_NPG_GITHUB_URL:=https://github.com/wtsi-npg} -WSI_NPG_BUILD_BRANCH=${WSI_NPG_BUILD_BRANCH:=devel} +# WSI_NPG_BUILD_BRANCH is undefined outside of pull request, ie on push. +if [ -z ${WSI_NPG_BUILD_BRANCH} ] +then + if [ "$WSI_NPG_GITHUB_REPO_OWNER" = "wtsi-npg" ] + then + WSI_NPG_BUILD_BRANCH=master + else + WSI_NPG_BUILD_BRANCH=devel + fi +fi # The first argument is the install base for NPG modules, enabling them to be # installed independently of CPAN dependencies. E.g. for cases where we want From 88d7bbcf4f55e4e85c3c809f762a07309b8eb745 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 5 Dec 2023 14:35:52 +0000 Subject: [PATCH 02/28] Generalised auto-generator for samplesheets. This generator was writted for MiSeq instrument format. Will have to be extended to include NovaSeqX format. This pull request, while not changing the current functionality, opens a way to extend the generator to other formats. --- bin/npg_samplesheet4MiSeq | 2 +- lib/npg/samplesheet/auto.pm | 107 +++++++++++++++++++++++++++--------- t/47-npg_samplesheet_auto.t | 27 +++++++-- 3 files changed, 106 insertions(+), 30 deletions(-) diff --git a/bin/npg_samplesheet4MiSeq b/bin/npg_samplesheet4MiSeq index c97cc99f..ae85ee56 100755 --- a/bin/npg_samplesheet4MiSeq +++ b/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(); diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index bcc061e9..267eaf17 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -7,6 +7,7 @@ use File::Basename; use Readonly; use File::Copy; use File::Spec::Functions; +use Carp; use npg::samplesheet; use npg_tracking::Schema; @@ -17,8 +18,11 @@ with q(MooseX::Log::Log4perl); our $VERSION = '0'; +Readonly::Scalar my $MISEQ_INSTRUMENT_FORMAT => 'MiSeq'; Readonly::Scalar my $DEFAULT_SLEEP => 90; +##no critic (Subroutines::ProhibitUnusedPrivateSubroutine) + =head1 NAME npg::samplesheet::auto @@ -30,12 +34,12 @@ npg::samplesheet::auto use npg::samplesheet::auto; use Log::Log4perl qw(:easy); BEGIN{ Log::Log4perl->easy_init({level=>$INFO,}); } - npg::samplesheet::auto->new()->loop(); + npg::samplesheet::auto->new(instrument_format => 'MiSeq')->loop(); =head1 DESCRIPTION -Class for creating Illumina MiSeq samplesheets automatically -for runs which are pending. +Class for creating Illumina samplesheets automatically for runs which are +pending. Currently is implemented only for MiSeq instruments' =head1 SUBROUTINES/METHODS @@ -65,6 +69,16 @@ sub _build_mlwh_schema { return WTSI::DNAP::Warehouse::Schema->connect(); } +=head2 instrument_format + +=cut + +has 'instrument_format' => ( + 'isa' => 'Str', + 'is' => 'ro', + 'default' => $MISEQ_INSTRUMENT_FORMAT, +); + =head2 sleep_interval =cut @@ -75,6 +89,24 @@ has 'sleep_interval' => ( 'default' => $DEFAULT_SLEEP, ); +=head2 BUILD + +Tests that a valid instrument format is used. + +=cut + +sub BUILD { + my $self = shift; + if ($self->instrument_format ne $MISEQ_INSTRUMENT_FORMAT) { + my $m = sprintf + 'Samplesheet auto-generator is not implemented for %s instrument format', + $self->instrument_format; + $self->log->fatal($m); + croak $m; + } + return; +} + =head2 loop Repeat the process step with the intervening sleep interval. @@ -96,34 +128,30 @@ of them if one does not already exist. sub process { my $self = shift; + my $rt = $self->_pending->run_statuses->search({iscurrent=>1}) ->related_resultset(q(run)); my $rs = $rt->search( - {q(run.id_instrument_format) => $self->_miseq->id_instrument_format}); - $self->log->debug( $rs->count. q[ ] .($self->_miseq->model). + {q(run.id_instrument_format) => $self->_instr_format_obj->id_instrument_format}); + $self->log->debug( $rs->count. q[ ] .($self->_instr_format_obj->model). q[ runs marked as ] .($self->_pending->description)); - while(my$r=$rs->next){ + + while(my$r=$rs->next) { # Loop over pending runs for this instrument format; + 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 $o = $ss->output; - my $generate_new = 1; - - if(-e $o) { - my $other_id_run = _id_run_from_samplesheet($o); - if ($other_id_run && $other_id_run == $id_run) { - $self->log->info(qq($o already exists for $id_run)); - $generate_new = 0; - } else { - $self->log->info(qq(Will move existing $o)); - _move_samplesheet($o); - } - } + my $method_name = + '_valid_samplesheet_file_exists_for_' . $self->instrument_format; + my $generate_new = !$self->$method_name($ss, $id_run); if ($generate_new) { + # Do not overwrite existing file if it exists. + my $o = $ss->output; + $self->_move_samplesheet_if_needed($o); try { $ss->process; $self->log->info(qq($o created for run ).($r->id_run)); @@ -133,17 +161,23 @@ sub process { } } } + return; } -has '_miseq' => ( +has '_instr_format_obj' => ( 'is' => 'ro', 'lazy_build' => 1, ); -sub _build__miseq { +sub _build__instr_format_obj { my $self=shift; - return $self->npg_tracking_schema->resultset(q(InstrumentFormat)) - ->find({q(model)=>q(MiSeq)}); + my $row = $self->npg_tracking_schema->resultset(q(InstrumentFormat)) + ->find({q(model)=>$self->instrument_format}); + if (!$row) { + croak sprintf 'Instrument format %s is not registered', + $self->instrument_format; + } + return $row; } has '_pending' => ( @@ -169,8 +203,14 @@ sub _id_run_from_samplesheet { return $id_run; } -sub _move_samplesheet { - my $file_path = shift; +sub _move_samplesheet_if_needed { + my ($self, $file_path) = @_; + + if (!-e $file_path) { + return; + } + + $self->log->info(qq(Will move existing $file_path)); my($filename, $dirname) = fileparse($file_path); $dirname =~ s/\/$//smx; #drop last forward slash if any @@ -186,6 +226,21 @@ sub _move_samplesheet { return; } +sub _valid_samplesheet_file_exists_for_MiSeq {##no critic (NamingConventions::Capitalization) + my ($self, $ss_object, $id_run) = @_; + + my $o = $ss_object->output; + if(-e $o) { + my $other_id_run = _id_run_from_samplesheet($o); + if ($other_id_run && $other_id_run == $id_run) { + $self->log->info(qq($o already exists for $id_run)); + return 1; + } + } + + return; +} + __PACKAGE__->meta->make_immutable; 1; @@ -216,6 +271,8 @@ __END__ =item Try::Tiny +=item Carp + =item npg_tracking::Schema =item npg::samplesheet diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t index 3e0c5e70..813e2baa 100644 --- a/t/47-npg_samplesheet_auto.t +++ b/t/47-npg_samplesheet_auto.t @@ -1,9 +1,10 @@ use strict; use warnings; -use Test::More tests => 9; +use Test::More tests => 12; use Test::Exception; use File::Temp qw/ tempdir /; use Moose::Meta::Class; +use Log::Log4perl qw(:easy); use_ok('npg::samplesheet::auto'); @@ -16,8 +17,17 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema]); my $sm; lives_ok { $sm = npg::samplesheet::auto->new( npg_tracking_schema => $schema, - mlwh_schema => $schema_wh) } 'miseq monitor object'; + mlwh_schema => $schema_wh) } 'MiSeq monitor object'; isa_ok($sm, 'npg::samplesheet::auto'); + is ($sm->instrument_format, 'MiSeq', 'default instrument format is MiSeq'); + + throws_ok { npg::samplesheet::auto->new( + npg_tracking_schema => $schema, + mlwh_schema => $schema_wh, + instrument_format => 'NovaSeq' + )} + qr/Samplesheet auto-generator is not implemented for NovaSeq instrument format/, + 'MiSeq error for an invalid instrument format'; } { @@ -30,9 +40,18 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema]); { my $dir = tempdir(UNLINK => 1); + + my $sm = npg::samplesheet::auto->new( + npg_tracking_schema => $schema, + mlwh_schema => $schema_wh + ); + my $file = join q[/], $dir, 'myfile'; `touch $file`; - npg::samplesheet::auto::_move_samplesheet($file); + lives_ok { + $sm->_move_samplesheet_if_needed($file . '_some'); + } 'OK to call with a file path that does not exist'; + $sm->_move_samplesheet_if_needed($file); ok(!-e $file, 'original file does not exist'); ok(-e $file.'_invalid', 'file has been moved'); @@ -42,7 +61,7 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema]); $file = join q[/], $sdir, 'myfile'; `touch $file`; my $new_file = join q[/], $sdir . '_old', 'myfile_invalid'; - npg::samplesheet::auto::_move_samplesheet($file); + $sm->_move_samplesheet_if_needed($file); ok(!-e $file, 'original file does not exist'); ok(-e $new_file, 'moved file is in samplesheet_old directory'); } From 0d9dbf9ec1e3f4d49cae3b087c95a7ba65ed29a2 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 5 Dec 2023 18:06:54 +0000 Subject: [PATCH 03/28] Removed provisions for XML driver in samplesheet generation. XML driver for st::api::lims was removed some time ago... The build method the 'lims' attribute is simplified since only the ml_warehouse driver is now used. --- lib/npg/samplesheet.pm | 37 +++++++++++-------------------------- t/47-samplesheet.t | 19 ++----------------- 2 files changed, 13 insertions(+), 43 deletions(-) diff --git a/lib/npg/samplesheet.pm b/lib/npg/samplesheet.pm index e80fab86..1c342174 100755 --- a/lib/npg/samplesheet.pm +++ b/lib/npg/samplesheet.pm @@ -69,19 +69,6 @@ Readonly::Scalar my $DEFAULT_LIMS_DRIVER_TYPE => 'ml_warehouse'; ####################### Public attributes ######################## ################################################################## -=head2 lims_driver_type - -LIMs driver type to use, defaults to ml_warehouse. - -=cut - -has 'lims_driver_type' => ( - 'isa' => 'Str', - 'required' => 0, - 'is' => 'ro', - 'default' => $DEFAULT_LIMS_DRIVER_TYPE, -); - =head2 id_run An optional attribute @@ -208,8 +195,12 @@ sub _build_run { An attribute, an array of st::api::lims type objects. +To generate a samplesheet for the whole run, provide an array of +at::api::lims objects for all lanes of the run. + This attribute should normally be provided by the caller via the -constuctor. If the attribute is not provided, it it built automatically. +constuctor. If the attribute is not provided, it is built automatically, +using the ml_warehouse lims driver. =cut @@ -221,19 +212,13 @@ has 'lims' => ( sub _build_lims { my $self=shift; - my $ref = {driver_type => $self->lims_driver_type}; - my $batch_id = $self->run->batch_id; - if ($self->lims_driver_type eq $DEFAULT_LIMS_DRIVER_TYPE) { - $ref->{'id_flowcell_lims'} = $batch_id; - $ref->{'mlwh_schema'} = $self->mlwh_schema; - } elsif ($self->lims_driver_type eq 'xml') { - $ref->{'batch_id'} = $batch_id; - } else { - croak sprintf 'Lazy-build for driver type %s is not inplemented', - $self->lims_driver_type; - } + my $run_lims = st::api::lims->new( + driver_type => $DEFAULT_LIMS_DRIVER_TYPE, + id_flowcell_lims => $self->run->batch_id, + mlwh_schema => $self->mlwh_schema + ); - return [st::api::lims->new($ref)->children]; + return [$run_lims->children()]; }; =head2 output diff --git a/t/47-samplesheet.t b/t/47-samplesheet.t index a74dc5fc..f8753b25 100644 --- a/t/47-samplesheet.t +++ b/t/47-samplesheet.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 12; +use Test::More tests => 11; use Test::LongString; use Test::Exception; use File::Slurp; @@ -26,22 +26,8 @@ local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q(t/data/samplesheet); my $dir = tempdir( CLEANUP => 1 ); -subtest 'error on an unknown driver type' => sub { - plan tests => 1; - - throws_ok { - npg::samplesheet->new( - lims_driver_type => 'foo', - repository => $dir, - npg_tracking_schema => $schema, - mlwh_schema => $mlwh_schema, - id_run => 7007)->lims() - } qr/Lazy-build for driver type foo is not inplemented/, - 'error with the driver type for which LIMS objects cannot be built'; -}; - subtest 'simple tests for the default driver' => sub { - plan tests => 2; + plan tests => 1; my $ss = npg::samplesheet->new( repository => $dir, @@ -49,7 +35,6 @@ subtest 'simple tests for the default driver' => sub { mlwh_schema => $mlwh_schema, id_run => 7007 ); - is ($ss->lims_driver_type, 'ml_warehouse', 'correct default driver type'); my $lims = $ss->lims(); is (@{$lims}, 1, 'LIMS data for 1 lane is built'); }; From 90e3a074045904b1831553c0217ad623b9fe27a3 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 6 Dec 2023 11:35:01 +0000 Subject: [PATCH 04/28] Removed unused test data. Most likely, this file was never needed and ended up in the repo by mistake. --- t/data/st_api_lims_new/st/samples/1750.html | 57 --------------------- 1 file changed, 57 deletions(-) delete mode 100644 t/data/st_api_lims_new/st/samples/1750.html diff --git a/t/data/st_api_lims_new/st/samples/1750.html b/t/data/st_api_lims_new/st/samples/1750.html deleted file mode 100644 index 9ac02352..00000000 --- a/t/data/st_api_lims_new/st/samples/1750.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - Sequencescape : Login - - - - - -
- -
- -
- SEQUENCESCAPE 5.02.07 -
- Sample and study management for sequencing and genotyping at the Wellcome Trust Sanger Institute. -
-
-
-
-
- - - - - - - - - - - - - - - - - -
 
-
-
- -
-
- - - From 7baef57d1e3a7ecf07a3783bd9ab5f7a591af98e Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 6 Dec 2023 17:39:38 +0000 Subject: [PATCH 05/28] Tested the content of NovaSeqX samplesheet. Added tests for the content of generated samplesheets to drive DRAGEN analysis on-board. --- MANIFEST | 3 + t/47-npg_samplesheet_novaseq_xseries.t | 59 +- t/data/dbic_fixtures/300-Run.yml | 14 + t/data/dbic_fixtures/300-RunLane.yml | 41 + t/data/dbic_fixtures/400-RunStatus.yml | 6 + t/data/dbic_fixtures/400-TagRun.yml | 20 + t/data/fixtures_lims_wh/000-Sample.yml | 5569 ++++++++++++ t/data/fixtures_lims_wh/000-Study.yml | 121 + t/data/fixtures_lims_wh/100-IseqFlowcell.yml | 7827 +++++++++++++++++ .../231206_47995_NVX1_A_ssbatch98292.csv | 202 + ...231206_47995_NVX1_A_ssbatch98292_align.csv | 298 + ...1206_47995_NVX1_A_ssbatch98292_varcall.csv | 298 + 12 files changed, 14456 insertions(+), 2 deletions(-) create mode 100644 t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292.csv create mode 100644 t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_align.csv create mode 100644 t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_varcall.csv diff --git a/MANIFEST b/MANIFEST index d3945903..ba18d2b8 100644 --- a/MANIFEST +++ b/MANIFEST @@ -687,6 +687,9 @@ 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 diff --git a/t/47-npg_samplesheet_novaseq_xseries.t b/t/47-npg_samplesheet_novaseq_xseries.t index 15f5cedb..ddc3ec98 100644 --- a/t/47-npg_samplesheet_novaseq_xseries.t +++ b/t/47-npg_samplesheet_novaseq_xseries.t @@ -1,9 +1,10 @@ use strict; use warnings; -use Test::More tests => 2; +use Test::More tests => 3; use Test::Exception; use Moose::Meta::Class; use DateTime; +use Perl6::Slurp; use npg_testing::db; @@ -16,7 +17,7 @@ my $schema_tracking = $class->new_object({})->create_test_db( ); my $schema_wh = $class->new_object({})->create_test_db( - q[WTSI::DNAP::Warehouse::Schema] + q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh] ); my $date = DateTime->now()->strftime('%y%m%d'); @@ -116,4 +117,58 @@ subtest 'create the generator object, test simple attributes' => sub { 'error when the run is registered on the wrong instrument model'; }; +subtest 'generate a samplesheet' => sub { + plan tests => 6; + + my $file_name = '47995_NVX1_A_ssbatch98292.csv'; + my $compare_file_root = + 't/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292'; + + my $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + id_run => 47995, + file_name => $file_name + ); + + # The code creates a new samplesheet in the working directory. + # This will be changed in future. + $g->process(); + ok (-e $file_name, 'the samplesheet file exists'); + my $compare_file = $compare_file_root . '.csv'; + is (slurp($file_name), slurp($compare_file), + 'the samplesheet is generated correctly'); + unlink $file_name; + + $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + id_run => 47995, + file_name => $file_name, + align => 1, + keep_fastq => 1 + ); + $g->process(); + ok (-e $file_name, 'the samplesheet file exists'); + $compare_file = $compare_file_root . '_align.csv'; + is (slurp($file_name), slurp($compare_file), + 'the samplesheet is generated correctly'); + unlink $file_name; + + $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + id_run => 47995, + file_name => $file_name, + align => 1, + varcall => 'AllVariantCallers' + ); + $g->process(); + ok (-e $file_name, 'the samplesheet file exists'); + $compare_file = $compare_file_root . '_varcall.csv'; + is (slurp($file_name), slurp($compare_file), + 'the samplesheet is generated correctly'); + unlink $file_name; +}; + 1; diff --git a/t/data/dbic_fixtures/300-Run.yml b/t/data/dbic_fixtures/300-Run.yml index eb0798bd..c29e3854 100644 --- a/t/data/dbic_fixtures/300-Run.yml +++ b/t/data/dbic_fixtures/300-Run.yml @@ -314,3 +314,17 @@ is_paired: 0 priority: 1 team: 'RAD' +- actual_cycle_count: 318 + batch_id: 98292 + expected_cycle_count: 318 + flowcell_id: 22FCNFLT3 + folder_name: 20231017_LH00210_0012_B22FCNFLT3 + folder_path_glob: '/{export,nfs}/esa-sv-20201215-01/IL_seq_data/*/' + id_instrument: 69 + id_instrument_format: 12 + id_run: 47995 + id_run_pair: ~ + is_paired: 0 + priority: 1 + team: A + diff --git a/t/data/dbic_fixtures/300-RunLane.yml b/t/data/dbic_fixtures/300-RunLane.yml index 2f91c96b..f75fbbda 100644 --- a/t/data/dbic_fixtures/300-RunLane.yml +++ b/t/data/dbic_fixtures/300-RunLane.yml @@ -169,3 +169,44 @@ position: 8 tile_count: 120 tracks: 2 +- id_run: 47995 + id_run_lane: 53234 + position: 1 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53235 + position: 2 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53236 + position: 3 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53237 + position: 4 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53238 + position: 5 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53239 + position: 6 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53240 + position: 7 + tile_count: 704 + tracks: 1 +- id_run: 47995 + id_run_lane: 53241 + position: 8 + tile_count: 704 + tracks: 1 + diff --git a/t/data/dbic_fixtures/400-RunStatus.yml b/t/data/dbic_fixtures/400-RunStatus.yml index b5c9f7e6..b958ded3 100644 --- a/t/data/dbic_fixtures/400-RunStatus.yml +++ b/t/data/dbic_fixtures/400-RunStatus.yml @@ -341,3 +341,9 @@ id_run_status_dict: 20 id_user: 7 iscurrent: 1 +- date: 2023-10-17 13:30:49 + id_run: 47995 + id_run_status: 103933 + id_run_status_dict: 1 + id_user: 3 + iscurrent: 0 diff --git a/t/data/dbic_fixtures/400-TagRun.yml b/t/data/dbic_fixtures/400-TagRun.yml index a056af39..c10056a6 100644 --- a/t/data/dbic_fixtures/400-TagRun.yml +++ b/t/data/dbic_fixtures/400-TagRun.yml @@ -184,3 +184,23 @@ id_tag: 20 id_tag_run: 27685 id_user: 76 +- date: 2023-10-17 + id_run: 47995 + id_tag: 9 + id_tag_run: 27686 + id_user: 7 +- date: 2023-10-17 + id_run: 47995 + id_tag: 19 + id_tag_run: 27687 + id_user: 7 +- date: 2023-10-17 + id_run: 47995 + id_tag: 20 + id_tag_run: 27688 + id_user: 7 +- date: 2023-10-17 + id_run: 47995 + id_tag: 22 + id_tag_run: 27689 + id_user: 7 diff --git a/t/data/fixtures_lims_wh/000-Sample.yml b/t/data/fixtures_lims_wh/000-Sample.yml index 8fc7424f..8200f084 100644 --- a/t/data/fixtures_lims_wh/000-Sample.yml +++ b/t/data/fixtures_lims_wh/000-Sample.yml @@ -610,3 +610,5572 @@ supplier_name: ~ taxon_id: ~ uuid_sample_lims: 77145e3a-b4cf-11e7-abfd-68b599768938 +- accession_number: EGAN00001321692 + age: ~ + cell_type: ~ + cohort: DDD_cohort + common_name: Homo sapiens + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2012-10-10 12:55:33 + customer_measured_concentration: 100.0 + customer_measured_volume: 100.0 + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Blood + donor_id: DDD_MAIN5407888 + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: ~ + gender: Female + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1497836 + id_sample_tmp: 1478203 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 20:11:58 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: DDD_MAIN5407888 + organism: Homo sapiens + organism_part: ~ + phenotype: Not applicable + priority_level: ~ + public_name: ~ + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:03:33 + reference_genome: ~ + replicate: ~ + sample_type: ~ + sample_visibility: ~ + sanger_sample_id: DDD_MAIN5407888 + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: DDD_1_FR00569506 + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: c7613702-12d9-11e2-92d0-68b59976a382 +- accession_number: EGAN00001321167 + age: ~ + cell_type: ~ + cohort: DDD_cohort + common_name: Homo sapiens + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2012-11-27 10:54:38 + customer_measured_concentration: 100.0 + customer_measured_volume: 100.0 + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Blood + donor_id: DDD_MAIN5426807 + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: ~ + gender: Male + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1517975 + id_sample_tmp: 1498338 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 20:13:17 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: DDD_MAIN5426807 + organism: Homo sapiens + organism_part: ~ + phenotype: Not applicable + priority_level: ~ + public_name: ~ + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:07:07 + reference_genome: ~ + replicate: ~ + sample_type: ~ + sample_visibility: ~ + sanger_sample_id: DDD_MAIN5426807 + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: DDD_1_FR00569436 + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: d69c9208-3880-11e2-a3c1-68b59976a382 +- accession_number: EGAN00001293786 + age: ~ + cell_type: ~ + cohort: DDD_cohort + common_name: Homo sapiens + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2013-11-28 16:20:25 + customer_measured_concentration: 100.0 + customer_measured_volume: 100.0 + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Saliva + donor_id: DDD_MAIN5670657 + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: ~ + gender: Female + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1779062 + id_sample_tmp: 1757640 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 20:38:01 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: DDD_MAIN5670657 + organism: Homo sapiens + organism_part: ~ + phenotype: Not applicable + priority_level: ~ + public_name: ~ + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:43:16 + reference_genome: ~ + replicate: ~ + sample_type: ~ + sample_visibility: ~ + sanger_sample_id: DDD_MAIN5670657 + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: DDD_1_D500PK132121 + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: fcf76c50-5848-11e3-b034-68b59976a382 +- accession_number: EGAN00001293787 + age: ~ + cell_type: ~ + cohort: DDD_cohort + common_name: Homo sapiens + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2013-11-28 16:20:25 + customer_measured_concentration: 100.0 + customer_measured_volume: 100.0 + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Saliva + donor_id: DDD_MAIN5670663 + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: ~ + gender: Male + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1779068 + id_sample_tmp: 1757646 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 20:38:01 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: DDD_MAIN5670663 + organism: Homo sapiens + organism_part: ~ + phenotype: Not applicable + priority_level: ~ + public_name: ~ + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:43:16 + reference_genome: ~ + replicate: ~ + sample_type: ~ + sample_visibility: ~ + sanger_sample_id: DDD_MAIN5670663 + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: DDD_1_D500PK132132 + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: fd15c9c0-5848-11e3-b034-68b59976a382 +- accession_number: EGAN00001293788 + age: ~ + cell_type: ~ + cohort: DDD_cohort + common_name: Homo sapiens + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2013-12-05 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cell_type: ~ + cohort: ~ + common_name: Homo sapiens + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: 0 + control_type: ~ + country_of_origin: not provided + created: 2023-09-28 09:00:28 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: not provided + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: ~ + donor_id: PD37586k + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: ~ + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 9296984 + id_sample_tmp: 9172504 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2023-09-28 09:00:28 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: 6050STDY14355648 + organism: ~ + organism_part: ~ + phenotype: ~ + priority_level: ~ + public_name: ~ + purification_method: ~ + purified: ~ + recorded_at: 2023-09-28 09:00:30 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: ~ + sanger_sample_id: 6050STDY14355648 + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: USUII_FF17PE + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: 78b50402-5ddd-11ee-b137-024224dd57f4 + diff --git a/t/data/fixtures_lims_wh/000-Study.yml b/t/data/fixtures_lims_wh/000-Study.yml index 420203dd..3e10bca7 100644 --- a/t/data/fixtures_lims_wh/000-Study.yml +++ b/t/data/fixtures_lims_wh/000-Study.yml @@ -134,3 +134,124 @@ study_type: Resequencing study_visibility: Hold uuid_study_lims: 8bedafde-5a6e-11e7-aeaa-68b59976a384 +- abbreviation: 6050STDY + abstract: 'Study somatic mutation in neurons.' + accession_number: EGAS00001004066 + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 1 + contaminated_human_dna: 0 + created: 2019-11-27 14:47:43 + data_access_group: cancer + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: other sequencing-based assay + data_release_strategy: not applicable + data_release_timing: never + deleted_at: ~ + description: "Bottleneck sequencing of human tissue." + ega_dac_accession_number: EGAC00001000000 + ega_policy_accession_number: EGAP00001000001 + ena_project_id: ~ + ethically_approved: 1 + faculty_sponsor: David Davidson + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 6050 + id_study_tmp: 5880 + last_updated: 2023-04-19 11:24:32 + name: 'Bottleneck Sequencing of Human Tissue - (WGS)' + prelim_id: ~ + recorded_at: 2023-04-19 11:24:32 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Bottleneck Sequencing Of Human Tissue (Wgs) + study_type: Cancer Genomics + study_visibility: Hold + uuid_study_lims: de933b7c-1124-11ea-a0f7-fa163e9d6485 +- abbreviation: 6751STDY + abstract: Investigating the driver landscape. + accession_number: EGAS00001005918 + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 1 + contaminated_human_dna: 0 + created: 2022-01-06 12:51:48 + data_access_group: cancer + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genotyping or cytogenetics + data_release_strategy: not applicable + data_release_timing: never + deleted_at: ~ + description: 'Targeted NanoSeq.' + ega_dac_accession_number: EGAC00001000000 + ega_policy_accession_number: EGAP00001000001 + ena_project_id: ~ + ethically_approved: 1 + faculty_sponsor: John Johnson + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 6751 + id_study_tmp: 6592 + last_updated: 2023-04-14 13:29:10 + name: Targeted NanoSeq_Synovium + prelim_id: ~ + recorded_at: 2023-04-14 13:29:10 + reference_genome: Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Targeted NanoSeq_Synovium + study_type: Cancer Genomics + study_visibility: Hold + uuid_study_lims: 696db2e8-6eef-11ec-8245-fa163eea3084 +- abbreviation: BGE + abstract: N/A + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 1 + contaminated_human_dna: 0 + created: 2023-11-02 15:51:12 + data_access_group: mercury + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genotyping or cytogenetics + data_release_strategy: not applicable + data_release_timing: never + deleted_at: ~ + description: 'This is a pilot study to assess a new pipeline.' + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: 0 + faculty_sponsor: Mary Thompson + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 7524 + id_study_tmp: 7469 + last_updated: 2023-11-02 15:51:36 + name: HG_BGE_Pilot + prelim_id: ~ + recorded_at: 2023-11-02 15:51:36 + reference_genome: Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: BGE Pilot + study_type: Exome Sequencing + study_visibility: Hold + uuid_study_lims: a5d57e6e-7997-11ee-b5c4-024293460e78 + diff --git a/t/data/fixtures_lims_wh/100-IseqFlowcell.yml b/t/data/fixtures_lims_wh/100-IseqFlowcell.yml index 0104ec6b..1a00b54a 100644 --- a/t/data/fixtures_lims_wh/100-IseqFlowcell.yml +++ b/t/data/fixtures_lims_wh/100-IseqFlowcell.yml @@ -772,3 +772,7830 @@ tag_set_id_lims: 142 tag_set_name: 'Magic Tag Group' +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289097 + id_library_lims: SQPP-7463-V:H8 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435526 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934716 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 64 + tag2_sequence: ATTGAGAG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 64 + tag_index: 1 + tag_sequence: CCTTCTCT + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289098 + id_library_lims: SQPP-7463-V:A9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435527 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934633 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 65 + tag2_sequence: CCCAATCA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 65 + tag_index: 2 + tag_sequence: TTTGAGGG + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289099 + id_library_lims: SQPP-7463-V:B9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435532 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934645 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 66 + tag2_sequence: TTGCAATC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 66 + tag_index: 3 + tag_sequence: GGCCTGGC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289100 + id_library_lims: SQPP-7463-V:C9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435518 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934657 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 67 + tag2_sequence: ATGGCAGC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 67 + tag_index: 4 + tag_sequence: AAAGTGAA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289101 + id_library_lims: SQPP-7463-V:D9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435529 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934669 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 68 + tag2_sequence: CACGCGAC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 68 + tag_index: 5 + tag_sequence: ACTCGAAA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289102 + id_library_lims: SQPP-7463-V:E9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435533 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934681 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 69 + tag2_sequence: ACCCAGAA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 69 + tag_index: 6 + tag_sequence: CGATTGCA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289103 + id_library_lims: SQPP-7463-V:F9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435534 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934693 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 70 + tag2_sequence: GTTTGGAA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 70 + tag_index: 7 + tag_sequence: GTAAGCGA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289104 + id_library_lims: SQPP-7463-V:G9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435516 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934705 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 71 + tag2_sequence: ACCACTGG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 71 + tag_index: 8 + tag_sequence: TTCTTCAG + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289105 + id_library_lims: SQPP-7463-V:H9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435517 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934717 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 72 + tag2_sequence: TTCCGGTG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 72 + tag_index: 9 + tag_sequence: CGTGGATA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289106 + id_library_lims: SQPP-7463-V:A10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435519 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934634 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 73 + tag2_sequence: AGTCGATG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 73 + tag_index: 10 + tag_sequence: CACTTTGC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289107 + id_library_lims: SQPP-7463-V:B10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435520 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934646 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 74 + tag2_sequence: GATGCGTC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 74 + tag_index: 11 + tag_sequence: GTGTCGGT + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + 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external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289109 + id_library_lims: SQPP-7463-V:D10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435522 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934670 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 76 + tag2_sequence: CAGACTGG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 76 + tag_index: 13 + tag_sequence: CTTTCGAC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289110 + id_library_lims: SQPP-7463-V:E10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435523 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934682 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 77 + tag2_sequence: ATAGCGTT + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 77 + tag_index: 14 + tag_sequence: GTGACCTA + tag_set_id_lims: 203 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tag_identifier: 78 + tag_index: 15 + tag_sequence: GTCCTAAC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289112 + id_library_lims: SQPP-7463-V:G10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435528 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934706 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 79 + tag2_sequence: AGTCTGCC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 79 + tag_index: 16 + tag_sequence: GTGCAGGG + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004573 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289113 + id_library_lims: SQPP-7463-V:H10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435531 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934718 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 80 + tag2_sequence: GCAACCTA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 80 + tag_index: 17 + tag_sequence: TGCGGTGT + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 70004573 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289095 + id_library_lims: NT1703488J + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 51702674 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: ~ + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: ~ + tag2_identifier: 888 + tag2_sequence: ACTGATGT + tag2_set_id_lims: 76 + tag2_set_name: Control Tag Group 888 + tag_identifier: ~ + tag_index: 888 + tag_sequence: TGTGCAGC + tag_set_id_lims: 76 + tag_set_name: Control Tag Group 888 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289115 + id_library_lims: SQPP-7463-V:H8 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435526 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934716 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 64 + tag2_sequence: ATTGAGAG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 64 + tag_index: 1 + tag_sequence: CCTTCTCT + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289116 + id_library_lims: SQPP-7463-V:A9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435527 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934633 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 65 + tag2_sequence: CCCAATCA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 65 + tag_index: 2 + tag_sequence: TTTGAGGG + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289117 + id_library_lims: SQPP-7463-V:B9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435532 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934645 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 66 + tag2_sequence: TTGCAATC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 66 + tag_index: 3 + tag_sequence: GGCCTGGC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289118 + id_library_lims: SQPP-7463-V:C9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435518 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934657 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 67 + tag2_sequence: ATGGCAGC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 67 + tag_index: 4 + tag_sequence: AAAGTGAA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289119 + 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Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289122 + id_library_lims: SQPP-7463-V:G9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435516 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934705 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 71 + tag2_sequence: ACCACTGG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 71 + tag_index: 8 + tag_sequence: TTCTTCAG + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289123 + id_library_lims: SQPP-7463-V:H9 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435517 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934717 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 72 + tag2_sequence: TTCCGGTG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 72 + tag_index: 9 + tag_sequence: CGTGGATA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289124 + id_library_lims: SQPP-7463-V:A10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435519 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934634 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 73 + tag2_sequence: AGTCGATG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 73 + tag_index: 10 + tag_sequence: CACTTTGC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289125 + id_library_lims: SQPP-7463-V:B10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435520 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934646 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 74 + tag2_sequence: GATGCGTC + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 74 + tag_index: 11 + tag_sequence: GTGTCGGT + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289126 + id_library_lims: SQPP-7463-V:C10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435521 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934658 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 75 + tag2_sequence: ACATTCTA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 75 + tag_index: 12 + tag_sequence: ACGTAACA + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289127 + id_library_lims: SQPP-7463-V:D10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435522 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934670 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 76 + tag2_sequence: CAGACTGG + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 76 + tag_index: 13 + tag_sequence: CTTTCGAC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289128 + id_library_lims: SQPP-7463-V:E10 + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 8435523 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 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8435524 + id_study_tmp: 6592 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 65934694 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Targeted NanoSeq Pulldown Twist + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 78 + tag2_sequence: TACGCCGA + tag2_set_id_lims: 202 + tag2_set_name: TS_pWGSD_UDI96_i5 + tag_identifier: 78 + tag_index: 15 + tag_sequence: GTCCTAAC + tag_set_id_lims: 203 + tag_set_name: TS_pWGSD_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: TE-95148282 + cost_code: S4360 + entity_id_lims: 70004574 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289130 + 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entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289114 + id_library_lims: NT1703488J + id_lims: SQSCP + id_pool_lims: NT1825568J + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 51702674 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: ~ + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: ~ + tag2_identifier: 888 + tag2_sequence: ACTGATGT + tag2_set_id_lims: 76 + tag2_set_name: Control Tag Group 888 + tag_identifier: ~ + tag_index: 888 + tag_sequence: TGTGCAGC + tag_set_id_lims: 76 + tag_set_name: Control Tag Group 888 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289133 + id_library_lims: NT1825792P + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171573 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723082 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 5 + tag2_sequence: AGAAGCCC + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 5 + tag_index: 1 + tag_sequence: TTGATTCC + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289134 + id_library_lims: NT1825793Q + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171574 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723083 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 13 + tag2_sequence: ACCTAACT + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 13 + tag_index: 2 + tag_sequence: CATCATTT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289135 + id_library_lims: NT1825794R + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171575 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723084 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 29 + tag2_sequence: GCTAATTG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 29 + tag_index: 3 + tag_sequence: ATATGCGC + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289136 + id_library_lims: NT1825795S + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171576 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723085 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 37 + tag2_sequence: GGTAGGTG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 37 + tag_index: 4 + tag_sequence: GTAAATGC + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289137 + id_library_lims: NT1825796T + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171577 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723086 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 45 + tag2_sequence: AAATTCAC + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 45 + tag_index: 5 + tag_sequence: TTAGTAGA + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289138 + id_library_lims: NT1825797U + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171578 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723087 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 53 + tag2_sequence: CTGGATTT + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 53 + tag_index: 6 + tag_sequence: CTGATGCT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289139 + id_library_lims: NT1825798V + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171579 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723088 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 61 + tag2_sequence: TACTGCCG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 61 + tag_index: 7 + tag_sequence: CTTGCGTG + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289140 + id_library_lims: NT1825799W + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171580 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723089 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 69 + tag2_sequence: CATTTATC + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 69 + tag_index: 8 + tag_sequence: CTGTCACA + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289141 + id_library_lims: NT1825800V + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171581 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723090 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 77 + tag2_sequence: AGTTGGAG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 77 + tag_index: 9 + tag_sequence: GCCTAGGG + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004575 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289142 + id_library_lims: NT1825801W + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171582 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723091 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq 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150 + manual_qc: 1 + pipeline_id_lims: ~ + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:08 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: ~ + tag2_identifier: 888 + tag2_sequence: ACTGATGT + tag2_set_id_lims: 76 + tag2_set_name: Control Tag Group 888 + tag_identifier: ~ + tag_index: 888 + tag_sequence: TGTGCAGC + tag_set_id_lims: 76 + tag_set_name: Control Tag Group 888 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004576 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289144 + id_library_lims: NT1825792P + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171573 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + 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flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289150 + id_library_lims: NT1825798V + id_lims: SQSCP + id_pool_lims: NT1825802A + id_sample_tmp: 9171579 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69723088 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 61 + tag2_sequence: TACTGCCG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 61 + tag_index: 7 + tag_sequence: CTTGCGTG + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004576 + 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tag_index: 888 + tag_sequence: TGTGCAGC + tag_set_id_lims: 76 + tag_set_name: Control Tag Group 888 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289155 + id_library_lims: NT1825817H + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172483 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725419 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 1 + tag2_sequence: ATGCGACT + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 1 + tag_index: 1 + tag_sequence: CGGAGACA + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289156 + id_library_lims: NT1825818I + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172484 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725420 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 2 + tag2_sequence: TCACAAAC + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 2 + tag_index: 2 + tag_sequence: GTTAACGT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289157 + id_library_lims: NT1825819J + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172485 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725421 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 3 + tag2_sequence: AGGAGAAA + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 3 + tag_index: 3 + tag_sequence: CATTTATT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289158 + id_library_lims: NT1825820C + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172486 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725422 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 4 + tag2_sequence: TCGGCAAA + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 4 + tag_index: 4 + tag_sequence: TTAGCGCA + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289159 + id_library_lims: NT1825821D + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172487 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725423 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + 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position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 26 + tag2_sequence: ACACATAT + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 26 + tag_index: 7 + tag_sequence: TTTGCAAA + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289162 + id_library_lims: NT1825824G + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172490 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725426 + loading_concentration: 150 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NT1825828K + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172494 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725430 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 43 + tag2_sequence: CCTACTAA + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 43 + tag_index: 12 + tag_sequence: GATATGTG + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + 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Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289171 + id_library_lims: NT1825833H + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172499 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725435 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 60 + tag2_sequence: TGCCATCC + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 60 + tag_index: 17 + tag_sequence: CGCAACTG + 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tag_identifier: 62 + tag_index: 18 + tag_sequence: CATATTCT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289173 + id_library_lims: NT1825835J + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172501 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725437 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 73 + tag2_sequence: CATTGCAC + 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NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 75 + tag2_sequence: TGCATAAA + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 75 + tag_index: 21 + tag_sequence: GTTCAAAG + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004577 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289176 + id_library_lims: NT1825838M + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172504 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725440 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + 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position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 2 + tag2_sequence: TCACAAAC + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 2 + tag_index: 2 + tag_sequence: GTTAACGT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289180 + id_library_lims: NT1825819J + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172485 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725421 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 3 + tag2_sequence: AGGAGAAA + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 3 + tag_index: 3 + tag_sequence: CATTTATT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289181 + id_library_lims: NT1825820C + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172486 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + 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12289185 + id_library_lims: NT1825824G + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172490 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725426 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 27 + tag2_sequence: GAACCCTG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 27 + tag_index: 8 + tag_sequence: CTTAGAGT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + 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flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289187 + id_library_lims: NT1825826I + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172492 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725428 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 41 + tag2_sequence: ATGCACTG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 41 + tag_index: 10 + tag_sequence: CCTCCTAA + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + 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team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289190 + id_library_lims: NT1825829L + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172495 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725431 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 44 + tag2_sequence: ATAAACTT + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 44 + tag_index: 13 + tag_sequence: CATGAATC + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289191 + id_library_lims: NT1825830E + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172496 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725432 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 57 + tag2_sequence: AGGCCGTT + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 57 + tag_index: 14 + tag_sequence: AGTAGTAG + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289192 + id_library_lims: NT1825831F + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172497 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725433 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 200 + requested_insert_size_to: 1500 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 58 + tag2_sequence: ACCCTCCA + 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reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 62 + tag2_sequence: CGGACAAG + tag2_set_id_lims: 212 + tag2_set_name: pWGSA_UDI_tempi5s + tag_identifier: 62 + tag_index: 18 + tag_sequence: CATATTCT + tag_set_id_lims: 211 + tag_set_name: pWGSA_UDI_tempi7s + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 70004578 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289196 + id_library_lims: NT1825835J + id_lims: SQSCP + id_pool_lims: NT1825839N + id_sample_tmp: 9172501 + id_study_tmp: 5880 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69725437 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Duplex-Seq + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + 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v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289255 + id_library_lims: SQPP-34872-C:E3 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8283126 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510890 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 21 + tag2_sequence: AAGACGTC + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 21 + tag_index: 16 + tag_sequence: GGTACCTT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289256 + id_library_lims: SQPP-34872-C:F3 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8283130 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510902 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 22 + tag2_sequence: GGAGTACT + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 22 + tag_index: 17 + tag_sequence: AACGTTCC + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289257 + id_library_lims: SQPP-34872-C:G3 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8283138 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510914 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 23 + tag2_sequence: ACCGGCCA + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 23 + tag_index: 18 + tag_sequence: GCAGAATT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289258 + id_library_lims: SQPP-34872-C:H3 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8283144 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510926 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 24 + tag2_sequence: GTTAATTG + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 24 + tag_index: 19 + tag_sequence: ATGAGGCC + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289259 + id_library_lims: SQPP-34872-C:A4 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8283149 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510843 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist 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+ cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289264 + id_library_lims: SQPP-34872-C:F4 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284527 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510903 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 30 + tag2_sequence: TGACAAGC + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 30 + tag_index: 25 + tag_sequence: TTACAGGA + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289265 + id_library_lims: SQPP-34872-C:G4 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284530 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510915 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 31 + tag2_sequence: CTAGCTTG + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 31 + tag_index: 26 + tag_sequence: GGCATTCT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289266 + id_library_lims: SQPP-34872-C:A5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284548 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510844 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 33 + tag2_sequence: CCTGAACT + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 33 + tag_index: 27 + tag_sequence: TACCGAGG + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289267 + id_library_lims: SQPP-34872-C:C5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284553 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510868 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 35 + tag2_sequence: AGTAGAGA + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 35 + tag_index: 28 + tag_sequence: AGCCTCAT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289268 + id_library_lims: SQPP-34872-C:D5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284552 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510880 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 36 + tag2_sequence: GACGAGAG + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 36 + tag_index: 29 + tag_sequence: GATTCTGC + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289269 + id_library_lims: SQPP-34872-C:E5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284558 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510892 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 37 + tag2_sequence: AGACTTGG + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 37 + tag_index: 30 + tag_sequence: TCGTAGTG + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289270 + id_library_lims: SQPP-34872-C:F5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284561 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510904 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 38 + tag2_sequence: GAGTCCAA + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 38 + tag_index: 31 + tag_sequence: CTACGACA + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289271 + id_library_lims: SQPP-34872-C:G5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284565 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510916 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 39 + tag2_sequence: CTTAAGCC + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 39 + tag_index: 32 + tag_sequence: TAAGTGGT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289272 + id_library_lims: SQPP-34872-C:H5 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284577 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510928 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 40 + tag2_sequence: TCCGGATT + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 40 + tag_index: 33 + tag_sequence: CGGACAAC + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289273 + id_library_lims: SQPP-34872-C:A6 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284581 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510845 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 41 + tag2_sequence: CTGTATTA + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 41 + tag_index: 34 + tag_sequence: ATATGGAT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289274 + id_library_lims: SQPP-34872-C:B6 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284587 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510857 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 42 + tag2_sequence: TCACGCCG + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 42 + tag_index: 35 + tag_sequence: GCGCAAGC + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289275 + id_library_lims: SQPP-34872-C:C6 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284590 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510869 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 43 + tag2_sequence: ACTTACAT + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 43 + tag_index: 36 + tag_sequence: AAGATACT + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289276 + id_library_lims: SQPP-34872-C:D6 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284595 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510881 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 44 + tag2_sequence: GTCCGTGC + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 44 + tag_index: 37 + tag_sequence: GGAGCGTC + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: Twist_Human_Core_Exome_BI + cost_code: S4215 + entity_id_lims: 70004571 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289277 + id_library_lims: SQPP-34872-C:E6 + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 8284597 + id_study_tmp: 7469 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 69510893 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: Twist Pulldown + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: 100 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: 0 + tag2_identifier: 45 + tag2_sequence: AAGGTACC + tag2_set_id_lims: 207 + tag2_set_name: IDT for Illumina i5 UDI v1 + tag_identifier: 45 + tag_index: 38 + tag_sequence: ATGGCATG + tag_set_id_lims: 206 + tag_set_name: IDT for Illumina i7 UDI v1 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 70004571 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 150 + id_flowcell_lims: 98292 + id_iseq_flowcell_tmp: 12289239 + id_library_lims: NT1703488J + id_lims: SQSCP + id_pool_lims: NT1826338B + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2023-11-03 11:24:07 + legacy_library_id: 51702674 + loading_concentration: 150 + manual_qc: 1 + pipeline_id_lims: ~ + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2023-11-03 11:24:09 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 150 + spiked_phix_barcode: NT1815266Q + spiked_phix_percentage: 1 + suboptimal: ~ + tag2_identifier: 888 + tag2_sequence: ACTGATGT + tag2_set_id_lims: 76 + tag2_set_name: Control Tag Group 888 + tag_identifier: ~ + tag_index: 888 + tag_sequence: TGTGCAGC + tag_set_id_lims: 76 + tag_set_name: Control Tag Group 888 + team: Illumina-HTP + workflow: ~ + diff --git a/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292.csv b/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292.csv new file mode 100644 index 00000000..3478f9c2 --- /dev/null +++ b/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292.csv @@ -0,0 +1,202 @@ +[Header],,,, +FileFormatVersion,2,,, +RunName,47995_NVX1_A,,, +InstrumentPlatform,NovaSeqXSeries,,, +InstrumentType,NovaSeqXPlus,,, +,,,, +[Reads],,,, +Read1Cycles,151,,, +Read2Cycles,151,,, +Index1Cycles,8,,, +Index2Cycles,8,,, +,,,, +[Sequencing_Settings],,,, +,,,, +[BCLConvert_Settings],,,, 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+1,6751STDY13219545,CTTTCGAC,CAGACTGG,Y151;I8;I8;Y151 +2,6751STDY13219545,CTTTCGAC,CAGACTGG,Y151;I8;I8;Y151 +1,6751STDY13219546,GTGACCTA,ATAGCGTT,Y151;I8;I8;Y151 +2,6751STDY13219546,GTGACCTA,ATAGCGTT,Y151;I8;I8;Y151 +1,6751STDY13219547,GTCCTAAC,TACGCCGA,Y151;I8;I8;Y151 +2,6751STDY13219547,GTCCTAAC,TACGCCGA,Y151;I8;I8;Y151 +1,6751STDY13219549,CCTTCTCT,ATTGAGAG,Y151;I8;I8;Y151 +2,6751STDY13219549,CCTTCTCT,ATTGAGAG,Y151;I8;I8;Y151 +1,6751STDY13219550,TTTGAGGG,CCCAATCA,Y151;I8;I8;Y151 +2,6751STDY13219550,TTTGAGGG,CCCAATCA,Y151;I8;I8;Y151 +1,6751STDY13219551,GTGCAGGG,AGTCTGCC,Y151;I8;I8;Y151 +2,6751STDY13219551,GTGCAGGG,AGTCTGCC,Y151;I8;I8;Y151 +1,6751STDY13219552,ACTCGAAA,CACGCGAC,Y151;I8;I8;Y151 +2,6751STDY13219552,ACTCGAAA,CACGCGAC,Y151;I8;I8;Y151 +1,6751STDY13219554,TGCGGTGT,GCAACCTA,Y151;I8;I8;Y151 +2,6751STDY13219554,TGCGGTGT,GCAACCTA,Y151;I8;I8;Y151 +1,6751STDY13219555,GGCCTGGC,TTGCAATC,Y151;I8;I8;Y151 +2,6751STDY13219555,GGCCTGGC,TTGCAATC,Y151;I8;I8;Y151 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+7,DDD_MAIN5867091,GGACTTGG,CGCAGACG,Y151;I8;I8;Y151 +8,DDD_MAIN5867091,GGACTTGG,CGCAGACG,Y151;I8;I8;Y151 +7,DDD_MAIN5908825,ATGTAAGT,ACTCTATG,Y151;I8;I8;Y151 +8,DDD_MAIN5908825,ATGTAAGT,ACTCTATG,Y151;I8;I8;Y151 +7,DDD_MAIN5908944,AAGTCCAA,TATGAGTA,Y151;I8;I8;Y151 +8,DDD_MAIN5908944,AAGTCCAA,TATGAGTA,Y151;I8;I8;Y151 +7,DDD_MAIN5908952,ATCCACTG,AGGTGCGT,Y151;I8;I8;Y151 +8,DDD_MAIN5908952,ATCCACTG,AGGTGCGT,Y151;I8;I8;Y151 +7,DDD_MAIN5966748,GCTTGTCA,GAACATAC,Y151;I8;I8;Y151 +8,DDD_MAIN5966748,GCTTGTCA,GAACATAC,Y151;I8;I8;Y151 +7,DDD_MAIN6028474,TTGGACTC,GGAAGCAG,Y151;I8;I8;Y151 +8,DDD_MAIN6028474,TTGGACTC,GGAAGCAG,Y151;I8;I8;Y151 +7,DDD_MAIN6029045,TGGATCGA,GTGCGATA,Y151;I8;I8;Y151 +8,DDD_MAIN6029045,TGGATCGA,GTGCGATA,Y151;I8;I8;Y151 +1,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +2,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +3,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +4,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +5,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +6,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +7,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +8,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 diff --git a/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_align.csv b/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_align.csv new file mode 100644 index 00000000..37f30c87 --- /dev/null +++ b/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_align.csv @@ -0,0 +1,298 @@ +[Header],,,, +FileFormatVersion,2,,, +RunName,47995_NVX1_A,,, +InstrumentPlatform,NovaSeqXSeries,,, +InstrumentType,NovaSeqXPlus,,, +,,,, +[Reads],,,, +Read1Cycles,151,,, +Read2Cycles,151,,, +Index1Cycles,8,,, +Index2Cycles,8,,, +,,,, +[Sequencing_Settings],,,, +,,,, +[BCLConvert_Settings],,,, +SoftwareVersion,v4.1.7,,, +FastqCompressionFormat,gzip,,, +,,,, +[BCLConvert_Data],,,, +Lane,Sample_ID,Index,Index2,OverrideCycles 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+3,6050STDY14354630,CTTACTCA,TCTCGACC,Y151;I8;I8;Y151 +4,6050STDY14354630,CTTACTCA,TCTCGACC,Y151;I8;I8;Y151 +5,6050STDY14355627,CGGAGACA,ATGCGACT,Y151;I8;I8;Y151 +6,6050STDY14355627,CGGAGACA,ATGCGACT,Y151;I8;I8;Y151 +5,6050STDY14355628,GTTAACGT,TCACAAAC,Y151;I8;I8;Y151 +6,6050STDY14355628,GTTAACGT,TCACAAAC,Y151;I8;I8;Y151 +5,6050STDY14355629,CATTTATT,AGGAGAAA,Y151;I8;I8;Y151 +6,6050STDY14355629,CATTTATT,AGGAGAAA,Y151;I8;I8;Y151 +5,6050STDY14355630,TTAGCGCA,TCGGCAAA,Y151;I8;I8;Y151 +6,6050STDY14355630,TTAGCGCA,TCGGCAAA,Y151;I8;I8;Y151 +5,6050STDY14355631,TATTCGTA,CTGAAAGA,Y151;I8;I8;Y151 +6,6050STDY14355631,TATTCGTA,CTGAAAGA,Y151;I8;I8;Y151 +5,6050STDY14355632,CTAACTAG,GAAAGGTA,Y151;I8;I8;Y151 +6,6050STDY14355632,CTAACTAG,GAAAGGTA,Y151;I8;I8;Y151 +5,6050STDY14355633,TTTGCAAA,ACACATAT,Y151;I8;I8;Y151 +6,6050STDY14355633,TTTGCAAA,ACACATAT,Y151;I8;I8;Y151 +5,6050STDY14355634,CTTAGAGT,GAACCCTG,Y151;I8;I8;Y151 +6,6050STDY14355634,CTTAGAGT,GAACCCTG,Y151;I8;I8;Y151 +5,6050STDY14355635,GGTGGGAA,TAAACCCA,Y151;I8;I8;Y151 +6,6050STDY14355635,GGTGGGAA,TAAACCCA,Y151;I8;I8;Y151 +5,6050STDY14355636,CCTCCTAA,ATGCACTG,Y151;I8;I8;Y151 +6,6050STDY14355636,CCTCCTAA,ATGCACTG,Y151;I8;I8;Y151 +5,6050STDY14355637,TTTCCAGT,ATGCCAAA,Y151;I8;I8;Y151 +6,6050STDY14355637,TTTCCAGT,ATGCCAAA,Y151;I8;I8;Y151 +5,6050STDY14355638,GATATGTG,CCTACTAA,Y151;I8;I8;Y151 +6,6050STDY14355638,GATATGTG,CCTACTAA,Y151;I8;I8;Y151 +5,6050STDY14355639,CATGAATC,ATAAACTT,Y151;I8;I8;Y151 +6,6050STDY14355639,CATGAATC,ATAAACTT,Y151;I8;I8;Y151 +5,6050STDY14355640,AGTAGTAG,AGGCCGTT,Y151;I8;I8;Y151 +6,6050STDY14355640,AGTAGTAG,AGGCCGTT,Y151;I8;I8;Y151 +5,6050STDY14355641,GAGGGCCG,ACCCTCCA,Y151;I8;I8;Y151 +6,6050STDY14355641,GAGGGCCG,ACCCTCCA,Y151;I8;I8;Y151 +5,6050STDY14355642,TTGTCCAA,CGGATCCC,Y151;I8;I8;Y151 +6,6050STDY14355642,TTGTCCAA,CGGATCCC,Y151;I8;I8;Y151 +5,6050STDY14355643,CGCAACTG,TGCCATCC,Y151;I8;I8;Y151 +6,6050STDY14355643,CGCAACTG,TGCCATCC,Y151;I8;I8;Y151 +5,6050STDY14355644,CATATTCT,CGGACAAG,Y151;I8;I8;Y151 +6,6050STDY14355644,CATATTCT,CGGACAAG,Y151;I8;I8;Y151 +5,6050STDY14355645,GCGGAGAC,CATTGCAC,Y151;I8;I8;Y151 +6,6050STDY14355645,GCGGAGAC,CATTGCAC,Y151;I8;I8;Y151 +5,6050STDY14355646,TTGGGTGA,ATAAAGCG,Y151;I8;I8;Y151 +6,6050STDY14355646,TTGGGTGA,ATAAAGCG,Y151;I8;I8;Y151 +5,6050STDY14355647,GTTCAAAG,TGCATAAA,Y151;I8;I8;Y151 +6,6050STDY14355647,GTTCAAAG,TGCATAAA,Y151;I8;I8;Y151 +5,6050STDY14355648,TTAACTTA,GTCATCCT,Y151;I8;I8;Y151 +6,6050STDY14355648,TTAACTTA,GTCATCCT,Y151;I8;I8;Y151 +7,6278STDY12901037,GCACGGAC,GTCTCGCA,Y151;I8;I8;Y151 +8,6278STDY12901037,GCACGGAC,GTCTCGCA,Y151;I8;I8;Y151 +7,6278STDY12901046,GGTACCTT,AAGACGTC,Y151;I8;I8;Y151 +8,6278STDY12901046,GGTACCTT,AAGACGTC,Y151;I8;I8;Y151 +7,6278STDY12901051,AACGTTCC,GGAGTACT,Y151;I8;I8;Y151 +8,6278STDY12901051,AACGTTCC,GGAGTACT,Y151;I8;I8;Y151 +7,6278STDY12901061,GCAGAATT,ACCGGCCA,Y151;I8;I8;Y151 +8,6278STDY12901061,GCAGAATT,ACCGGCCA,Y151;I8;I8;Y151 +7,6278STDY12901069,ATGAGGCC,GTTAATTG,Y151;I8;I8;Y151 +8,6278STDY12901069,ATGAGGCC,GTTAATTG,Y151;I8;I8;Y151 +7,6278STDY12901078,ACTAAGAT,AACCGCGG,Y151;I8;I8;Y151 +8,6278STDY12901078,ACTAAGAT,AACCGCGG,Y151;I8;I8;Y151 +7,6278STDY12901100,GTCGGAGC,GGTTATAA,Y151;I8;I8;Y151 +8,6278STDY12901100,GTCGGAGC,GGTTATAA,Y151;I8;I8;Y151 +7,6278STDY12901101,CTTGGTAT,CCAAGTCC,Y151;I8;I8;Y151 +8,6278STDY12901101,CTTGGTAT,CCAAGTCC,Y151;I8;I8;Y151 +7,6278STDY12902768,TCCAACGC,TTGGACTT,Y151;I8;I8;Y151 +8,6278STDY12902768,TCCAACGC,TTGGACTT,Y151;I8;I8;Y151 +7,6278STDY12902770,CCGTGAAG,CAGTGGAT,Y151;I8;I8;Y151 +8,6278STDY12902770,CCGTGAAG,CAGTGGAT,Y151;I8;I8;Y151 +7,6278STDY12902777,TTACAGGA,TGACAAGC,Y151;I8;I8;Y151 +8,6278STDY12902777,TTACAGGA,TGACAAGC,Y151;I8;I8;Y151 +7,6278STDY12902780,GGCATTCT,CTAGCTTG,Y151;I8;I8;Y151 +8,6278STDY12902780,GGCATTCT,CTAGCTTG,Y151;I8;I8;Y151 +7,6278STDY12902798,TACCGAGG,CCTGAACT,Y151;I8;I8;Y151 +8,6278STDY12902798,TACCGAGG,CCTGAACT,Y151;I8;I8;Y151 +7,6278STDY12902802,AGCCTCAT,AGTAGAGA,Y151;I8;I8;Y151 +8,6278STDY12902802,AGCCTCAT,AGTAGAGA,Y151;I8;I8;Y151 +7,6278STDY12902803,GATTCTGC,GACGAGAG,Y151;I8;I8;Y151 +8,6278STDY12902803,GATTCTGC,GACGAGAG,Y151;I8;I8;Y151 +7,6278STDY12902808,TCGTAGTG,AGACTTGG,Y151;I8;I8;Y151 +8,6278STDY12902808,TCGTAGTG,AGACTTGG,Y151;I8;I8;Y151 +7,6278STDY12902811,CTACGACA,GAGTCCAA,Y151;I8;I8;Y151 +8,6278STDY12902811,CTACGACA,GAGTCCAA,Y151;I8;I8;Y151 +7,6278STDY12902815,TAAGTGGT,CTTAAGCC,Y151;I8;I8;Y151 +8,6278STDY12902815,TAAGTGGT,CTTAAGCC,Y151;I8;I8;Y151 +7,6278STDY12902827,CGGACAAC,TCCGGATT,Y151;I8;I8;Y151 +8,6278STDY12902827,CGGACAAC,TCCGGATT,Y151;I8;I8;Y151 +7,6278STDY12902831,ATATGGAT,CTGTATTA,Y151;I8;I8;Y151 +8,6278STDY12902831,ATATGGAT,CTGTATTA,Y151;I8;I8;Y151 +7,6278STDY12902837,GCGCAAGC,TCACGCCG,Y151;I8;I8;Y151 +8,6278STDY12902837,GCGCAAGC,TCACGCCG,Y151;I8;I8;Y151 +7,6278STDY12902840,AAGATACT,ACTTACAT,Y151;I8;I8;Y151 +8,6278STDY12902840,AAGATACT,ACTTACAT,Y151;I8;I8;Y151 +7,6278STDY12902845,GGAGCGTC,GTCCGTGC,Y151;I8;I8;Y151 +8,6278STDY12902845,GGAGCGTC,GTCCGTGC,Y151;I8;I8;Y151 +7,6278STDY12902847,ATGGCATG,AAGGTACC,Y151;I8;I8;Y151 +8,6278STDY12902847,ATGGCATG,AAGGTACC,Y151;I8;I8;Y151 +1,6751STDY13219539,TTCTTCAG,ACCACTGG,Y151;I8;I8;Y151 +2,6751STDY13219539,TTCTTCAG,ACCACTGG,Y151;I8;I8;Y151 +1,6751STDY13219540,CGTGGATA,TTCCGGTG,Y151;I8;I8;Y151 +2,6751STDY13219540,CGTGGATA,TTCCGGTG,Y151;I8;I8;Y151 +1,6751STDY13219541,AAAGTGAA,ATGGCAGC,Y151;I8;I8;Y151 +2,6751STDY13219541,AAAGTGAA,ATGGCAGC,Y151;I8;I8;Y151 +1,6751STDY13219542,CACTTTGC,AGTCGATG,Y151;I8;I8;Y151 +2,6751STDY13219542,CACTTTGC,AGTCGATG,Y151;I8;I8;Y151 +1,6751STDY13219543,GTGTCGGT,GATGCGTC,Y151;I8;I8;Y151 +2,6751STDY13219543,GTGTCGGT,GATGCGTC,Y151;I8;I8;Y151 +1,6751STDY13219544,ACGTAACA,ACATTCTA,Y151;I8;I8;Y151 +2,6751STDY13219544,ACGTAACA,ACATTCTA,Y151;I8;I8;Y151 +1,6751STDY13219545,CTTTCGAC,CAGACTGG,Y151;I8;I8;Y151 +2,6751STDY13219545,CTTTCGAC,CAGACTGG,Y151;I8;I8;Y151 +1,6751STDY13219546,GTGACCTA,ATAGCGTT,Y151;I8;I8;Y151 +2,6751STDY13219546,GTGACCTA,ATAGCGTT,Y151;I8;I8;Y151 +1,6751STDY13219547,GTCCTAAC,TACGCCGA,Y151;I8;I8;Y151 +2,6751STDY13219547,GTCCTAAC,TACGCCGA,Y151;I8;I8;Y151 +1,6751STDY13219549,CCTTCTCT,ATTGAGAG,Y151;I8;I8;Y151 +2,6751STDY13219549,CCTTCTCT,ATTGAGAG,Y151;I8;I8;Y151 +1,6751STDY13219550,TTTGAGGG,CCCAATCA,Y151;I8;I8;Y151 +2,6751STDY13219550,TTTGAGGG,CCCAATCA,Y151;I8;I8;Y151 +1,6751STDY13219551,GTGCAGGG,AGTCTGCC,Y151;I8;I8;Y151 +2,6751STDY13219551,GTGCAGGG,AGTCTGCC,Y151;I8;I8;Y151 +1,6751STDY13219552,ACTCGAAA,CACGCGAC,Y151;I8;I8;Y151 +2,6751STDY13219552,ACTCGAAA,CACGCGAC,Y151;I8;I8;Y151 +1,6751STDY13219554,TGCGGTGT,GCAACCTA,Y151;I8;I8;Y151 +2,6751STDY13219554,TGCGGTGT,GCAACCTA,Y151;I8;I8;Y151 +1,6751STDY13219555,GGCCTGGC,TTGCAATC,Y151;I8;I8;Y151 +2,6751STDY13219555,GGCCTGGC,TTGCAATC,Y151;I8;I8;Y151 +1,6751STDY13219556,CGATTGCA,ACCCAGAA,Y151;I8;I8;Y151 +2,6751STDY13219556,CGATTGCA,ACCCAGAA,Y151;I8;I8;Y151 +1,6751STDY13219557,GTAAGCGA,GTTTGGAA,Y151;I8;I8;Y151 +2,6751STDY13219557,GTAAGCGA,GTTTGGAA,Y151;I8;I8;Y151 +7,DDD_MAIN5407888,CCGCGGTT,AGCGCTAG,Y151;I8;I8;Y151 +8,DDD_MAIN5407888,CCGCGGTT,AGCGCTAG,Y151;I8;I8;Y151 +7,DDD_MAIN5426807,TAATACAG,ATATTCAC,Y151;I8;I8;Y151 +8,DDD_MAIN5426807,TAATACAG,ATATTCAC,Y151;I8;I8;Y151 +7,DDD_MAIN5670657,GGCTTAAG,TCGTGACC,Y151;I8;I8;Y151 +8,DDD_MAIN5670657,GGCTTAAG,TCGTGACC,Y151;I8;I8;Y151 +7,DDD_MAIN5670663,AATCCGGA,CTACAGTT,Y151;I8;I8;Y151 +8,DDD_MAIN5670663,AATCCGGA,CTACAGTT,Y151;I8;I8;Y151 +7,DDD_MAIN5678531,CCAAGTCT,AAGGATGA,Y151;I8;I8;Y151 +8,DDD_MAIN5678531,CCAAGTCT,AAGGATGA,Y151;I8;I8;Y151 +7,DDD_MAIN5710659,TTATAACC,GATATCGA,Y151;I8;I8;Y151 +8,DDD_MAIN5710659,TTATAACC,GATATCGA,Y151;I8;I8;Y151 +7,DDD_MAIN5714029,CGGCGTGA,GCGCCTGT,Y151;I8;I8;Y151 +8,DDD_MAIN5714029,CGGCGTGA,GCGCCTGT,Y151;I8;I8;Y151 +7,DDD_MAIN5867091,GGACTTGG,CGCAGACG,Y151;I8;I8;Y151 +8,DDD_MAIN5867091,GGACTTGG,CGCAGACG,Y151;I8;I8;Y151 +7,DDD_MAIN5908825,ATGTAAGT,ACTCTATG,Y151;I8;I8;Y151 +8,DDD_MAIN5908825,ATGTAAGT,ACTCTATG,Y151;I8;I8;Y151 +7,DDD_MAIN5908944,AAGTCCAA,TATGAGTA,Y151;I8;I8;Y151 +8,DDD_MAIN5908944,AAGTCCAA,TATGAGTA,Y151;I8;I8;Y151 +7,DDD_MAIN5908952,ATCCACTG,AGGTGCGT,Y151;I8;I8;Y151 +8,DDD_MAIN5908952,ATCCACTG,AGGTGCGT,Y151;I8;I8;Y151 +7,DDD_MAIN5966748,GCTTGTCA,GAACATAC,Y151;I8;I8;Y151 +8,DDD_MAIN5966748,GCTTGTCA,GAACATAC,Y151;I8;I8;Y151 +7,DDD_MAIN6028474,TTGGACTC,GGAAGCAG,Y151;I8;I8;Y151 +8,DDD_MAIN6028474,TTGGACTC,GGAAGCAG,Y151;I8;I8;Y151 +7,DDD_MAIN6029045,TGGATCGA,GTGCGATA,Y151;I8;I8;Y151 +8,DDD_MAIN6029045,TGGATCGA,GTGCGATA,Y151;I8;I8;Y151 +1,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +2,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +3,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +4,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +5,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +6,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +7,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +8,phiX_for_spiked_buffers,TGTGCAGC,ACTGATGT,Y151;I8;I8;Y151 +,,,, +[DragenGermline_Settings],,,, +SoftwareVersion,v4.1.7,,, +MapAlignOutFormat,cram,,, +KeepFastq,TRUE,,, +,,,, +[DragenGermline_Data],,,, +Sample_ID,ReferenceGenomeDir,VariantCallingMode,, +6050STDY14354621,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354622,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354623,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354624,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354625,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354626,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354627,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354628,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354629,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14354630,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355627,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355628,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355629,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355630,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355631,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355632,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355633,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355634,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355635,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355636,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355637,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355638,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355639,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355640,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355641,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355642,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355643,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355644,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355645,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355646,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355647,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6050STDY14355648,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901037,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901046,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901051,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901061,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901069,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901078,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901100,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12901101,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902768,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902770,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902777,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902780,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902798,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902802,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902803,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902808,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902811,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902815,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902827,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902831,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902837,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902840,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902845,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6278STDY12902847,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219539,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219540,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219541,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219542,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219543,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219544,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219545,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219546,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219547,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219549,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219550,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219551,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219552,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219554,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219555,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219556,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +6751STDY13219557,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5407888,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5426807,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5670657,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5670663,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5678531,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5710659,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5714029,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5867091,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5908825,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5908944,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5908952,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN5966748,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN6028474,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +DDD_MAIN6029045,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,None,, +,,,, diff --git a/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_varcall.csv b/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_varcall.csv new file mode 100644 index 00000000..a7b01319 --- /dev/null +++ b/t/data/samplesheet/dragen/231206_47995_NVX1_A_ssbatch98292_varcall.csv @@ -0,0 +1,298 @@ +[Header],,,, +FileFormatVersion,2,,, +RunName,47995_NVX1_A,,, +InstrumentPlatform,NovaSeqXSeries,,, +InstrumentType,NovaSeqXPlus,,, +,,,, +[Reads],,,, +Read1Cycles,151,,, +Read2Cycles,151,,, +Index1Cycles,8,,, +Index2Cycles,8,,, +,,,, +[Sequencing_Settings],,,, +,,,, +[BCLConvert_Settings],,,, +SoftwareVersion,v4.1.7,,, +FastqCompressionFormat,gzip,,, +,,,, +[BCLConvert_Data],,,, +Lane,Sample_ID,Index,Index2,OverrideCycles +3,6050STDY14354621,TTGATTCC,AGAAGCCC,Y151;I8;I8;Y151 +4,6050STDY14354621,TTGATTCC,AGAAGCCC,Y151;I8;I8;Y151 +3,6050STDY14354622,CATCATTT,ACCTAACT,Y151;I8;I8;Y151 +4,6050STDY14354622,CATCATTT,ACCTAACT,Y151;I8;I8;Y151 +3,6050STDY14354623,ATATGCGC,GCTAATTG,Y151;I8;I8;Y151 +4,6050STDY14354623,ATATGCGC,GCTAATTG,Y151;I8;I8;Y151 +3,6050STDY14354624,GTAAATGC,GGTAGGTG,Y151;I8;I8;Y151 +4,6050STDY14354624,GTAAATGC,GGTAGGTG,Y151;I8;I8;Y151 +3,6050STDY14354625,TTAGTAGA,AAATTCAC,Y151;I8;I8;Y151 +4,6050STDY14354625,TTAGTAGA,AAATTCAC,Y151;I8;I8;Y151 +3,6050STDY14354626,CTGATGCT,CTGGATTT,Y151;I8;I8;Y151 +4,6050STDY14354626,CTGATGCT,CTGGATTT,Y151;I8;I8;Y151 +3,6050STDY14354627,CTTGCGTG,TACTGCCG,Y151;I8;I8;Y151 +4,6050STDY14354627,CTTGCGTG,TACTGCCG,Y151;I8;I8;Y151 +3,6050STDY14354628,CTGTCACA,CATTTATC,Y151;I8;I8;Y151 +4,6050STDY14354628,CTGTCACA,CATTTATC,Y151;I8;I8;Y151 +3,6050STDY14354629,GCCTAGGG,AGTTGGAG,Y151;I8;I8;Y151 +4,6050STDY14354629,GCCTAGGG,AGTTGGAG,Y151;I8;I8;Y151 +3,6050STDY14354630,CTTACTCA,TCTCGACC,Y151;I8;I8;Y151 +4,6050STDY14354630,CTTACTCA,TCTCGACC,Y151;I8;I8;Y151 +5,6050STDY14355627,CGGAGACA,ATGCGACT,Y151;I8;I8;Y151 +6,6050STDY14355627,CGGAGACA,ATGCGACT,Y151;I8;I8;Y151 +5,6050STDY14355628,GTTAACGT,TCACAAAC,Y151;I8;I8;Y151 +6,6050STDY14355628,GTTAACGT,TCACAAAC,Y151;I8;I8;Y151 +5,6050STDY14355629,CATTTATT,AGGAGAAA,Y151;I8;I8;Y151 +6,6050STDY14355629,CATTTATT,AGGAGAAA,Y151;I8;I8;Y151 +5,6050STDY14355630,TTAGCGCA,TCGGCAAA,Y151;I8;I8;Y151 +6,6050STDY14355630,TTAGCGCA,TCGGCAAA,Y151;I8;I8;Y151 +5,6050STDY14355631,TATTCGTA,CTGAAAGA,Y151;I8;I8;Y151 +6,6050STDY14355631,TATTCGTA,CTGAAAGA,Y151;I8;I8;Y151 +5,6050STDY14355632,CTAACTAG,GAAAGGTA,Y151;I8;I8;Y151 +6,6050STDY14355632,CTAACTAG,GAAAGGTA,Y151;I8;I8;Y151 +5,6050STDY14355633,TTTGCAAA,ACACATAT,Y151;I8;I8;Y151 +6,6050STDY14355633,TTTGCAAA,ACACATAT,Y151;I8;I8;Y151 +5,6050STDY14355634,CTTAGAGT,GAACCCTG,Y151;I8;I8;Y151 +6,6050STDY14355634,CTTAGAGT,GAACCCTG,Y151;I8;I8;Y151 +5,6050STDY14355635,GGTGGGAA,TAAACCCA,Y151;I8;I8;Y151 +6,6050STDY14355635,GGTGGGAA,TAAACCCA,Y151;I8;I8;Y151 +5,6050STDY14355636,CCTCCTAA,ATGCACTG,Y151;I8;I8;Y151 +6,6050STDY14355636,CCTCCTAA,ATGCACTG,Y151;I8;I8;Y151 +5,6050STDY14355637,TTTCCAGT,ATGCCAAA,Y151;I8;I8;Y151 +6,6050STDY14355637,TTTCCAGT,ATGCCAAA,Y151;I8;I8;Y151 +5,6050STDY14355638,GATATGTG,CCTACTAA,Y151;I8;I8;Y151 +6,6050STDY14355638,GATATGTG,CCTACTAA,Y151;I8;I8;Y151 +5,6050STDY14355639,CATGAATC,ATAAACTT,Y151;I8;I8;Y151 +6,6050STDY14355639,CATGAATC,ATAAACTT,Y151;I8;I8;Y151 +5,6050STDY14355640,AGTAGTAG,AGGCCGTT,Y151;I8;I8;Y151 +6,6050STDY14355640,AGTAGTAG,AGGCCGTT,Y151;I8;I8;Y151 +5,6050STDY14355641,GAGGGCCG,ACCCTCCA,Y151;I8;I8;Y151 +6,6050STDY14355641,GAGGGCCG,ACCCTCCA,Y151;I8;I8;Y151 +5,6050STDY14355642,TTGTCCAA,CGGATCCC,Y151;I8;I8;Y151 +6,6050STDY14355642,TTGTCCAA,CGGATCCC,Y151;I8;I8;Y151 +5,6050STDY14355643,CGCAACTG,TGCCATCC,Y151;I8;I8;Y151 +6,6050STDY14355643,CGCAACTG,TGCCATCC,Y151;I8;I8;Y151 +5,6050STDY14355644,CATATTCT,CGGACAAG,Y151;I8;I8;Y151 +6,6050STDY14355644,CATATTCT,CGGACAAG,Y151;I8;I8;Y151 +5,6050STDY14355645,GCGGAGAC,CATTGCAC,Y151;I8;I8;Y151 +6,6050STDY14355645,GCGGAGAC,CATTGCAC,Y151;I8;I8;Y151 +5,6050STDY14355646,TTGGGTGA,ATAAAGCG,Y151;I8;I8;Y151 +6,6050STDY14355646,TTGGGTGA,ATAAAGCG,Y151;I8;I8;Y151 +5,6050STDY14355647,GTTCAAAG,TGCATAAA,Y151;I8;I8;Y151 +6,6050STDY14355647,GTTCAAAG,TGCATAAA,Y151;I8;I8;Y151 +5,6050STDY14355648,TTAACTTA,GTCATCCT,Y151;I8;I8;Y151 +6,6050STDY14355648,TTAACTTA,GTCATCCT,Y151;I8;I8;Y151 +7,6278STDY12901037,GCACGGAC,GTCTCGCA,Y151;I8;I8;Y151 +8,6278STDY12901037,GCACGGAC,GTCTCGCA,Y151;I8;I8;Y151 +7,6278STDY12901046,GGTACCTT,AAGACGTC,Y151;I8;I8;Y151 +8,6278STDY12901046,GGTACCTT,AAGACGTC,Y151;I8;I8;Y151 +7,6278STDY12901051,AACGTTCC,GGAGTACT,Y151;I8;I8;Y151 +8,6278STDY12901051,AACGTTCC,GGAGTACT,Y151;I8;I8;Y151 +7,6278STDY12901061,GCAGAATT,ACCGGCCA,Y151;I8;I8;Y151 +8,6278STDY12901061,GCAGAATT,ACCGGCCA,Y151;I8;I8;Y151 +7,6278STDY12901069,ATGAGGCC,GTTAATTG,Y151;I8;I8;Y151 +8,6278STDY12901069,ATGAGGCC,GTTAATTG,Y151;I8;I8;Y151 +7,6278STDY12901078,ACTAAGAT,AACCGCGG,Y151;I8;I8;Y151 +8,6278STDY12901078,ACTAAGAT,AACCGCGG,Y151;I8;I8;Y151 +7,6278STDY12901100,GTCGGAGC,GGTTATAA,Y151;I8;I8;Y151 +8,6278STDY12901100,GTCGGAGC,GGTTATAA,Y151;I8;I8;Y151 +7,6278STDY12901101,CTTGGTAT,CCAAGTCC,Y151;I8;I8;Y151 +8,6278STDY12901101,CTTGGTAT,CCAAGTCC,Y151;I8;I8;Y151 +7,6278STDY12902768,TCCAACGC,TTGGACTT,Y151;I8;I8;Y151 +8,6278STDY12902768,TCCAACGC,TTGGACTT,Y151;I8;I8;Y151 +7,6278STDY12902770,CCGTGAAG,CAGTGGAT,Y151;I8;I8;Y151 +8,6278STDY12902770,CCGTGAAG,CAGTGGAT,Y151;I8;I8;Y151 +7,6278STDY12902777,TTACAGGA,TGACAAGC,Y151;I8;I8;Y151 +8,6278STDY12902777,TTACAGGA,TGACAAGC,Y151;I8;I8;Y151 +7,6278STDY12902780,GGCATTCT,CTAGCTTG,Y151;I8;I8;Y151 +8,6278STDY12902780,GGCATTCT,CTAGCTTG,Y151;I8;I8;Y151 +7,6278STDY12902798,TACCGAGG,CCTGAACT,Y151;I8;I8;Y151 +8,6278STDY12902798,TACCGAGG,CCTGAACT,Y151;I8;I8;Y151 +7,6278STDY12902802,AGCCTCAT,AGTAGAGA,Y151;I8;I8;Y151 +8,6278STDY12902802,AGCCTCAT,AGTAGAGA,Y151;I8;I8;Y151 +7,6278STDY12902803,GATTCTGC,GACGAGAG,Y151;I8;I8;Y151 +8,6278STDY12902803,GATTCTGC,GACGAGAG,Y151;I8;I8;Y151 +7,6278STDY12902808,TCGTAGTG,AGACTTGG,Y151;I8;I8;Y151 +8,6278STDY12902808,TCGTAGTG,AGACTTGG,Y151;I8;I8;Y151 +7,6278STDY12902811,CTACGACA,GAGTCCAA,Y151;I8;I8;Y151 +8,6278STDY12902811,CTACGACA,GAGTCCAA,Y151;I8;I8;Y151 +7,6278STDY12902815,TAAGTGGT,CTTAAGCC,Y151;I8;I8;Y151 +8,6278STDY12902815,TAAGTGGT,CTTAAGCC,Y151;I8;I8;Y151 +7,6278STDY12902827,CGGACAAC,TCCGGATT,Y151;I8;I8;Y151 +8,6278STDY12902827,CGGACAAC,TCCGGATT,Y151;I8;I8;Y151 +7,6278STDY12902831,ATATGGAT,CTGTATTA,Y151;I8;I8;Y151 +8,6278STDY12902831,ATATGGAT,CTGTATTA,Y151;I8;I8;Y151 +7,6278STDY12902837,GCGCAAGC,TCACGCCG,Y151;I8;I8;Y151 +8,6278STDY12902837,GCGCAAGC,TCACGCCG,Y151;I8;I8;Y151 +7,6278STDY12902840,AAGATACT,ACTTACAT,Y151;I8;I8;Y151 +8,6278STDY12902840,AAGATACT,ACTTACAT,Y151;I8;I8;Y151 +7,6278STDY12902845,GGAGCGTC,GTCCGTGC,Y151;I8;I8;Y151 +8,6278STDY12902845,GGAGCGTC,GTCCGTGC,Y151;I8;I8;Y151 +7,6278STDY12902847,ATGGCATG,AAGGTACC,Y151;I8;I8;Y151 +8,6278STDY12902847,ATGGCATG,AAGGTACC,Y151;I8;I8;Y151 +1,6751STDY13219539,TTCTTCAG,ACCACTGG,Y151;I8;I8;Y151 +2,6751STDY13219539,TTCTTCAG,ACCACTGG,Y151;I8;I8;Y151 +1,6751STDY13219540,CGTGGATA,TTCCGGTG,Y151;I8;I8;Y151 +2,6751STDY13219540,CGTGGATA,TTCCGGTG,Y151;I8;I8;Y151 +1,6751STDY13219541,AAAGTGAA,ATGGCAGC,Y151;I8;I8;Y151 +2,6751STDY13219541,AAAGTGAA,ATGGCAGC,Y151;I8;I8;Y151 +1,6751STDY13219542,CACTTTGC,AGTCGATG,Y151;I8;I8;Y151 +2,6751STDY13219542,CACTTTGC,AGTCGATG,Y151;I8;I8;Y151 +1,6751STDY13219543,GTGTCGGT,GATGCGTC,Y151;I8;I8;Y151 +2,6751STDY13219543,GTGTCGGT,GATGCGTC,Y151;I8;I8;Y151 +1,6751STDY13219544,ACGTAACA,ACATTCTA,Y151;I8;I8;Y151 +2,6751STDY13219544,ACGTAACA,ACATTCTA,Y151;I8;I8;Y151 +1,6751STDY13219545,CTTTCGAC,CAGACTGG,Y151;I8;I8;Y151 +2,6751STDY13219545,CTTTCGAC,CAGACTGG,Y151;I8;I8;Y151 +1,6751STDY13219546,GTGACCTA,ATAGCGTT,Y151;I8;I8;Y151 +2,6751STDY13219546,GTGACCTA,ATAGCGTT,Y151;I8;I8;Y151 +1,6751STDY13219547,GTCCTAAC,TACGCCGA,Y151;I8;I8;Y151 +2,6751STDY13219547,GTCCTAAC,TACGCCGA,Y151;I8;I8;Y151 +1,6751STDY13219549,CCTTCTCT,ATTGAGAG,Y151;I8;I8;Y151 +2,6751STDY13219549,CCTTCTCT,ATTGAGAG,Y151;I8;I8;Y151 +1,6751STDY13219550,TTTGAGGG,CCCAATCA,Y151;I8;I8;Y151 +2,6751STDY13219550,TTTGAGGG,CCCAATCA,Y151;I8;I8;Y151 +1,6751STDY13219551,GTGCAGGG,AGTCTGCC,Y151;I8;I8;Y151 +2,6751STDY13219551,GTGCAGGG,AGTCTGCC,Y151;I8;I8;Y151 +1,6751STDY13219552,ACTCGAAA,CACGCGAC,Y151;I8;I8;Y151 +2,6751STDY13219552,ACTCGAAA,CACGCGAC,Y151;I8;I8;Y151 +1,6751STDY13219554,TGCGGTGT,GCAACCTA,Y151;I8;I8;Y151 +2,6751STDY13219554,TGCGGTGT,GCAACCTA,Y151;I8;I8;Y151 +1,6751STDY13219555,GGCCTGGC,TTGCAATC,Y151;I8;I8;Y151 +2,6751STDY13219555,GGCCTGGC,TTGCAATC,Y151;I8;I8;Y151 +1,6751STDY13219556,CGATTGCA,ACCCAGAA,Y151;I8;I8;Y151 +2,6751STDY13219556,CGATTGCA,ACCCAGAA,Y151;I8;I8;Y151 +1,6751STDY13219557,GTAAGCGA,GTTTGGAA,Y151;I8;I8;Y151 +2,6751STDY13219557,GTAAGCGA,GTTTGGAA,Y151;I8;I8;Y151 +7,DDD_MAIN5407888,CCGCGGTT,AGCGCTAG,Y151;I8;I8;Y151 +8,DDD_MAIN5407888,CCGCGGTT,AGCGCTAG,Y151;I8;I8;Y151 +7,DDD_MAIN5426807,TAATACAG,ATATTCAC,Y151;I8;I8;Y151 +8,DDD_MAIN5426807,TAATACAG,ATATTCAC,Y151;I8;I8;Y151 +7,DDD_MAIN5670657,GGCTTAAG,TCGTGACC,Y151;I8;I8;Y151 +8,DDD_MAIN5670657,GGCTTAAG,TCGTGACC,Y151;I8;I8;Y151 +7,DDD_MAIN5670663,AATCCGGA,CTACAGTT,Y151;I8;I8;Y151 +8,DDD_MAIN5670663,AATCCGGA,CTACAGTT,Y151;I8;I8;Y151 +7,DDD_MAIN5678531,CCAAGTCT,AAGGATGA,Y151;I8;I8;Y151 +8,DDD_MAIN5678531,CCAAGTCT,AAGGATGA,Y151;I8;I8;Y151 +7,DDD_MAIN5710659,TTATAACC,GATATCGA,Y151;I8;I8;Y151 +8,DDD_MAIN5710659,TTATAACC,GATATCGA,Y151;I8;I8;Y151 +7,DDD_MAIN5714029,CGGCGTGA,GCGCCTGT,Y151;I8;I8;Y151 +8,DDD_MAIN5714029,CGGCGTGA,GCGCCTGT,Y151;I8;I8;Y151 +7,DDD_MAIN5867091,GGACTTGG,CGCAGACG,Y151;I8;I8;Y151 +8,DDD_MAIN5867091,GGACTTGG,CGCAGACG,Y151;I8;I8;Y151 +7,DDD_MAIN5908825,ATGTAAGT,ACTCTATG,Y151;I8;I8;Y151 +8,DDD_MAIN5908825,ATGTAAGT,ACTCTATG,Y151;I8;I8;Y151 +7,DDD_MAIN5908944,AAGTCCAA,TATGAGTA,Y151;I8;I8;Y151 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+DDD_MAIN6029045,hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2,AllVariantCallers,, +,,,, From 7b3e06e4e37a9fbb4e637f9ceccc2c5c3fcece64 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 15 Dec 2023 13:36:20 +0000 Subject: [PATCH 06/28] Improved samplesheet generation for NovaSeqX. Commented out code deleted. Attributes and methods are ordered more logically. Some private accesors are converted to public. Documentation improved. Added index_read_length and read_length attributes so that these values can be set by the caller. --- bin/npg_samplesheet_generator_NovaSeqXSeries | 60 ++- lib/npg/samplesheet/novaseq_xseries.pm | 450 ++++++++++--------- t/47-npg_samplesheet_novaseq_xseries.t | 5 +- 3 files changed, 271 insertions(+), 244 deletions(-) diff --git a/bin/npg_samplesheet_generator_NovaSeqXSeries b/bin/npg_samplesheet_generator_NovaSeqXSeries index b96df3b3..d759b0cc 100755 --- a/bin/npg_samplesheet_generator_NovaSeqXSeries +++ b/bin/npg_samplesheet_generator_NovaSeqXSeries @@ -27,26 +27,40 @@ npg_samplesheet_generator_NovaSeqXSeries C - displays help message and exists - C - variant calling mode, defaults to C, other valid options - C and C C - LIMS batch identifier, optional C - NPG run ID, optional; if supplied, the record for this run should exists in the run tracking database + + C - + an optional list of read lengths, forward first, reverse + second; currently both default to 151 + + C - + 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 - a boolean option, false by default; if set, the DRAGEN germline analysis section is added to the file if suitable samples are present - C - an option to keep FASTQ files for aligned data, false - default - C - DRAGEN analysis can deal with a limited - number of distinct configurations. Set this attribute if - processing not on-board. + + C - variant calling mode, defaults to C, other valid options + C and C + + C - + an option to keep FASTQ files for aligned data, false by + default + + C - + DRAGEN analysis can deal with a limited number of distinct + configurations. Set this attribute if processing off-board. =head1 DESCRIPTION -Samplesheet generation to initiate DRAGEN analysis of data sequenced -on the NovaSeq Series X Illumina instrument. +Generates a samplesheet for the NovaSeq Series X Illumina instrument and +DRAGEN analysis. =head1 EXIT STATUS @@ -56,37 +70,13 @@ 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 diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index abed8cf5..39faf030 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -8,7 +8,6 @@ use Carp; use Text::CSV; use List::MoreUtils qw(any none uniq); use List::Util qw(first max); -use Getopt::Long; use Pod::Usage; use DateTime; use Data::UUID; @@ -87,7 +86,7 @@ L ( 'run should exists in the run tracking database', ); + =head2 batch_id LIMS batch ID, an optional attribute. If not set, the C attribute @@ -158,9 +158,60 @@ sub _build_batch_id { return $batch_id; } + +=head2 index_read_length + +An array containing the length of the first and the second (if applicable) +indexing read. + +If not set, is computed as the longest first and second barcode as reported +by the LIMS system. + +=cut + +has 'index_read_length' => ( + 'isa' => 'ArrayRef', + 'is' => 'ro', + 'lazy_build' => 1, + 'required' => 0, + 'documentation' => 'An array containing the length of the first and the ' . + 'second (if applicable) indexing read..', +); +sub _build_index_read_length { + my $self = shift; + my $index1_length = max ( + map { length $_->[$LIST_INDEX_TAG1] } $self->products + ); + my $index2_length = max ( + map { length $_->[$LIST_INDEX_TAG2] } $self->products + ); + return [$index1_length, $index2_length]; +} + + +=head2 read_length + +An array containing the length of the forward and the reverse read. +If not set, is currently hardcoded as [151, 151]. + +=cut + +has 'read_length' => ( + 'isa' => 'ArrayRef', + 'is' => 'ro', + 'lazy_build' => 1, + 'required' => 0, + 'documentation' => 'An array containing the length of the forward and the ' . + 'reverse read', +); +sub _build_read_length { + return [$READ1_LENGTH, $READ2_LENGTH]; +} + + =head2 align -A boolean option, false by default; if set, the DRAGEN germline iand/or +A boolean option, false by default; if set, the DRAGEN germline and/or RNA analysis is added to the samplesheet if suitable samples are present. =cut @@ -174,6 +225,7 @@ has 'align' => ( 'suitable samples are present.', ); + =head2 keep_fastq A boolean option to keep FASTQ files for aligned data, false by default. @@ -188,6 +240,7 @@ has 'keep_fastq' => ( 'by default.', ); + =head2 varcall Variant calling mode, defaults to C, other valid options are @@ -204,6 +257,7 @@ has 'varcall' => ( 'options are SmallVariantCaller and AllVariantCallers', ); + =head2 dragen_max_number_of_configs =cut @@ -218,12 +272,6 @@ has 'dragen_max_number_of_configs' => ( 'processing not on-board', ); -has '_current_number_of_configs' => ( - 'isa' => 'Int', - 'is' => 'rw', - 'default' => 0, - 'required' => 0, -); =head2 npg_tracking_schema @@ -241,6 +289,7 @@ sub _build_npg_tracking_schema { return npg_tracking::Schema->connect(); } + =head2 mlwh_schema DBIx Schema object for the mlwh database. @@ -257,6 +306,7 @@ sub _build_mlwh_schema { return WTSI::DNAP::Warehouse::Schema->connect(); } + =head2 run DBIx object for a row in the run table of the tracking database. @@ -287,6 +337,7 @@ sub _build_run { return $run; } + =head2 lims An attribute, an array of C type objects. @@ -311,6 +362,7 @@ sub _build_lims { )->children()]; } + =head2 run_name =cut @@ -328,7 +380,8 @@ sub _build_run_name { my $run_name; if ($self->has_id_run()) { # Embed instrument's Sanger network name and slot - $run_name = sprintf '%s_%s_%s', $self->id_run, $self->run->instrument->name, $self->get_instrument_side; + $run_name = sprintf '%s_%s_%s', $self->id_run, + $self->run->instrument->name, $self->get_instrument_side; } else { # Run is not tracked, generate a placeholder ID my $ug = Data::UUID->new(); @@ -340,6 +393,7 @@ sub _build_run_name { return $run_name; } + =head2 file_name =cut @@ -369,18 +423,12 @@ sub _build_file_name { return $file_name; } -has '_all_lines' => ( - 'isa' => 'ArrayRef', - 'is' => 'ro', - 'default' => sub { return []; } , - 'required' => 0, -); -sub _add_line { - my ($self, @columns) = @_; - push @{$self->_all_lines()}, @columns ? \@columns : []; - return; -} +=head2 products + +A list of products as given by LIMS, a read-only accessor. + +=cut has '_products' => ( 'isa' => 'ArrayRef', @@ -418,22 +466,6 @@ sub _build__products { return \@products; } -has '_index_reads_length' => ( - 'isa' => 'ArrayRef', - 'is' => 'ro', - 'lazy_build' => 1, - 'required' => 0, -); -sub _build__index_reads_length { - my $self = shift; - my $index1_length = max ( - map { length $_->[$LIST_INDEX_TAG1] } $self->products - ); - my $index2_length = max ( - map { length $_->[$LIST_INDEX_TAG2] } $self->products - ); - return [$index1_length, $index2_length]; -} =head2 process @@ -504,6 +536,41 @@ sub process { return; } +=head2 add_common_headers + +Adds the top-level header section. + +=cut + +sub add_common_headers { + my $self = shift; + + my ($index1_length, $index2_length) = @{$self->index_read_length()}; + $self->_add_line('[Header]'); + $self->_add_line(q[FileFormatVersion], 2); + $self->_add_line(q[RunName], $self->run_name); + $self->_add_line(qw(InstrumentPlatform NovaSeqXSeries)); + $self->_add_line(qw(InstrumentType NovaSeqXPlus)); + $self->_add_line(); + + # Reads section + $self->_add_line('[Reads]'); + $self->_add_line(q[Read1Cycles], $self->read_length()->[0]); + $self->_add_line(q[Read2Cycles], $self->read_length()->[1]); + if ($index1_length) { + $self->_add_line('Index1Cycles', $index1_length); + if ($index2_length) { + $self->_add_line('Index2Cycles', $index2_length); + } + } + + $self->_add_line(); + $self->_add_line('[Sequencing_Settings]'); + + return; +} + + =head2 add_bclconvert_section Adds BCLConvert_Settings and BCLConvert_Data sections. @@ -513,49 +580,31 @@ has not been added. The latter happens if the number of unique configurations for BCLConvert exceeds the maximum number of allowed configurations. In this case no further analysis sections should be added to the samplesheet. +The OverrideCycles column specifies the sequencing and indexing cycles to be +used when processing the sequencing data. Must adhere to the following +requirements: + +- Must be same number of fields (delimited by semicolon) as sequencing and + indexing reads specified in RunInfo.xml or Reads section. + +- Indexing reads are specified with I, sequencing reads are specified with + Y, UMI cycles are specified with U, and trimmed reads are specified with N. + +- The number of cycles specified for each read must equal the number of cycles + specified for that read in the RunInfo.xml file. + +- Only one Y or I sequence can be specified per read. + =cut sub add_bclconvert_section { my $self = shift; - my ($index1_length, $index2_length) = @{$self->_index_reads_length()}; + my ($index1_length, $index2_length) = @{$self->index_read_length()}; my @lines = (); push @lines, ['[BCLConvert_Settings]']; push @lines, [q[SoftwareVersion], $self->dragen_software_version]; - - # Not clear what CLI analysis option thie corresponds to. - # Looks likely to be a list of lanes to run a tag collision check. - # According to @srl, bcl-covert tries to correct one error by default - # but it checks the tags allow this, i.e. that they all differ by at least - # 3 bases, if they don't it disables the error correction - # $add_line->(qw(CombinedIndexCollisionCheck 1;3;4;6)); - - # CreateFastqForIndexReads might be an option. Do we need these files? - # $add_line->(qw(CreateFastqForIndexReads 1)); - # When 1 will be appropriate for this trim? - # $add_line->(qw(TrimUMI 0)); - # dragen is the other compression options push @lines, [qw(FastqCompressionFormat gzip)]; - - # Barcode mismatch tolerances, the default is 1. - # These settings can be omitted. - #if ($index1_length) { - # $add_line->(qw(BarcodeMismatchesIndex1 1)); - # if ($index2_length) { - # $add_line->(qw(BarcodeMismatchesIndex2 1)); - # } - #} - - # Adapter trimming settings. The sequence of the Read 1 (or 2) adapter - # to be masked or trimmed. To trim multiple adapters, separate the sequences - # with a plus sign (+) indicating independent adapters that must be - # independently assessed for masking or trimming for each read. - # Characters must be A, C, G, or T. - # It seems that this settign can also be a column in teh data section - # - # $add_line->(qw(AdapterRead1 SOME)); - # $add_line->(qw(AdapterRead2 OTHER)); - push @lines, []; push @lines, ['[BCLConvert_Data]']; @@ -569,17 +618,6 @@ sub add_bclconvert_section { } push @lines, \@data_header; - # Override Cycles - Specifies the sequencing and indexing cycles to be used - # when processing the sequencing data. Must adhere to the - # following requirements: - # - Must be same number of fields (delimited by semicolon) as sequencing and - # indexing reads specified in RunInfo.xml or Reads section. - # - Indexing reads are specified with I, sequencing reads are specified with - # Y, UMI cycles are specified with U, and trimmed reads are specified with N. - # - The number of cycles specified for each read must equal the number of - # cycles specified for that read in the RunInfo.xml file. - # - Only one Y or I sequence can be specified per read. - my $index_override = sub { my ($max_length, $barcode) = @_; my $i_cycles_number = length $barcode; @@ -604,7 +642,7 @@ sub add_bclconvert_section { if ($index1_length) { my $i7 = $product->[$LIST_INDEX_TAG1]; push @product_data, $i7; - push @override_cycles, q[Y] . $READ1_LENGTH; + push @override_cycles, q[Y] . $self->read_length()->[0]; push @override_cycles, $index_override->($index1_length, $i7); if ($index2_length) { @@ -613,7 +651,7 @@ sub add_bclconvert_section { push @override_cycles, $index_override->($index2_length, $i5); } - push @override_cycles, q[Y] . $READ2_LENGTH; + push @override_cycles, q[Y] . $self->read_length()->[1]; } my $override_cycles_string = join q[;], @override_cycles; # Might be an empty string ... @@ -637,43 +675,108 @@ sub add_bclconvert_section { return scalar @lines; } -=head2 add_common_headers -Adds the top-level header section. +=head2 add_germline_section + +Conditionally adds the DragenGermline_Settings and DragenGermline_Data +sections. =cut -sub add_common_headers { +sub add_germline_section { my $self = shift; - my ($index1_length, $index2_length) = @{$self->_index_reads_length()}; - $self->_add_line('[Header]'); - $self->_add_line(q[FileFormatVersion], 2); - $self->_add_line(q[RunName], $self->run_name); - $self->_add_line(qw(InstrumentPlatform NovaSeqXSeries)); - # NovaSeqxPlus or NovaSeqX. - # If the run id is given, this should come from the tracking database - # when we fix the type there. - $self->_add_line(qw(InstrumentType NovaSeqXPlus)); - $self->_add_line(); + if (none { $self->varcall eq $_ } @VAR_CALL_MODES) { + croak 'Uknown mode for variang calling - ' . $self->varcall; + } - # Reads section - $self->_add_line('[Reads]'); - $self->_add_line(q[Read1Cycles], $READ1_LENGTH); - $self->_add_line(q[Read2Cycles], $READ2_LENGTH); - if ($index1_length) { - $self->_add_line('Index1Cycles', $index1_length); - if ($index2_length) { - $self->_add_line('Index2Cycles', $index2_length); + my @to_align = (); + my @ref_matches = keys %REFERENCE_MAPING; + my $distinct_configs = {}; + + foreach my $p ( $self->products() ) { + + my $r = $p->[$LIST_INDEX_REF]; + my $lib_type = $p->[$LIST_INDEX_LIBTYPE]; + + if ( can_do_alignment($r) && !(do_ref_rna_alignment_test($r) || + do_libtype_rna_alignment_test($lib_type) || + do_libtype_tenx_test($lib_type)) ) { + + my $match = first { $r =~ /$_/xms} @ref_matches; + if ($self->_can_add_sample($distinct_configs, $match)) { + # TODO Are all variant calling modes compatible with all + # references? + push @to_align, [$p->[1], $REFERENCE_MAPING{$match}, $self->varcall]; + } } } - $self->_add_line(); - $self->_add_line('[Sequencing_Settings]'); + if (@to_align) { - return; + $self->_add_line('[DragenGermline_Settings]'); + $self->_add_line(q[SoftwareVersion], $self->dragen_software_version); + $self->_add_line(qw(MapAlignOutFormat cram)); + # Accepted values are true or false. Not clear whether this can be + # set per sample. + $self->_add_line(q(KeepFastq), $self->keep_fastq ? 'TRUE' : 'FALSE'); + $self->_add_line(); + + $self->_add_line(qw([DragenGermline_Data])); + $self->_add_line(qw(Sample_ID ReferenceGenomeDir VariantCallingMode)); + $self->_add_samples(@to_align); + } + + return scalar @to_align; } + +=head2 add_rna_section + +Conditionally adds the DragenRNA_Settings and DragenRNA_Data sections. + +=cut + +sub add_rna_section { + my $self = shift; + + my @to_align = (); + my @ref_matches = keys %REFERENCE_MAPING; + my $distinct_configs = {}; + + foreach my $p ( $self->products() ) { + + my $r = $p->[$LIST_INDEX_REF]; + my $lib_type = $p->[$LIST_INDEX_LIBTYPE]; + + if ( can_do_alignment($r) && ( + do_ref_rna_alignment_test($r) || + do_libtype_rna_alignment_test($lib_type)) ) { + + my $match = first { $r =~ /$_/xms} @ref_matches; + if ($self->_can_add_sample($distinct_configs, $match)) { + push @to_align, [$p->[1], $REFERENCE_MAPING{$match}]; + } + } + } + + if (@to_align) { + $self->_add_line('[DragenRNA_Settings]'); + $self->_add_line(q(SoftwareVersion), $self->dragen_software_version); + $self->_add_line(qw(MapAlignOutFormat cram)); + $self->_add_line(q(KeepFastq), $self->keep_fastq ? 'TRUE' : 'FALSE'); + $self->_add_line(qw(RnaPipelineMode FullPipeline)); + $self->_add_line(); + + $self->_add_line('[DragenRNA_Data]'); + $self->_add_line(qw(Sample_ID ReferenceGenomeDir)); + $self->_add_samples(@to_align); + } + + return scalar @to_align; +} + + =head2 can_do_alignment =cut @@ -683,6 +786,7 @@ sub can_do_alignment { return $r && !($r =~ /Not suitable/xmsi); } + =head2 do_ref_rna_alignment_test =cut @@ -692,6 +796,7 @@ sub do_ref_rna_alignment_test { return any { $r =~ /$_/xmsi } @RNA_ANALYSES_REFS; } + =head2 do_libtype_rna_alignment_test =cut @@ -701,6 +806,7 @@ sub do_libtype_rna_alignment_test { return any { $lt =~ /$_/xmsi } @RNA_ANALYSES_LIB_TYPES; } + =head2 do_libtype_tenx_test =cut @@ -710,6 +816,7 @@ sub do_libtype_tenx_test { return any { $lt =~ /$_/xmsi } @TENX_ANALYSES_LIB_TYPES; } + =head2 get_instrument_side Consult run tags to determine which slot/side of the instrument this run is @@ -727,6 +834,32 @@ sub get_instrument_side { return $side; } +################################################################## +# Private attributes and methods # +################################################################## + +# A writable counter. +has '_current_number_of_configs' => ( + 'isa' => 'Int', + 'is' => 'rw', + 'default' => 0, + 'required' => 0, +); + + +has '_all_lines' => ( + 'isa' => 'ArrayRef', + 'is' => 'ro', + 'default' => sub { return []; } , + 'required' => 0, +); + + +sub _add_line { + my ($self, @columns) = @_; + push @{$self->_all_lines()}, @columns ? \@columns : []; + return; +} sub _add_samples { my ($self, @samples) = @_; @@ -742,6 +875,7 @@ sub _add_samples { return; } + sub _can_add_sample { my ($self, $distinct_configs, $config) = @_; @@ -762,104 +896,6 @@ sub _can_add_sample { return 1; } -=head2 add_germline_section - -Conditionally adds the DragenGermline_Settings and DragenGermline_Data -sections. - -=cut - -sub add_germline_section { - my $self = shift; - - if (none { $self->varcall eq $_ } @VAR_CALL_MODES) { - croak 'Uknown mode for variang calling - ' . $self->varcall; - } - - my @to_align = (); - my @ref_matches = keys %REFERENCE_MAPING; - my $distinct_configs = {}; - - foreach my $p ( $self->products() ) { - - my $r = $p->[$LIST_INDEX_REF]; - my $lib_type = $p->[$LIST_INDEX_LIBTYPE]; - - if ( can_do_alignment($r) && !(do_ref_rna_alignment_test($r) || - do_libtype_rna_alignment_test($lib_type) || - do_libtype_tenx_test($lib_type)) ) { - - my $match = first { $r =~ /$_/xms} @ref_matches; - if ($self->_can_add_sample($distinct_configs, $match)) { - # TODO Are all variant calling modes compatible with all - # references? - push @to_align, [$p->[1], $REFERENCE_MAPING{$match}, $self->varcall]; - } - } - } - - if (@to_align) { - - $self->_add_line('[DragenGermline_Settings]'); - $self->_add_line(q[SoftwareVersion], $self->dragen_software_version); - $self->_add_line(qw(MapAlignOutFormat cram)); - # Accepted values are true or false. Not clear whether this can be - # set per sample. - $self->_add_line(q(KeepFastq), $self->keep_fastq ? 'TRUE' : 'FALSE'); - $self->_add_line(); - - $self->_add_line(qw([DragenGermline_Data])); - $self->_add_line(qw(Sample_ID ReferenceGenomeDir VariantCallingMode)); - $self->_add_samples(@to_align); - } - - return scalar @to_align; -} - -=head2 add_rna_section - -Conditionally adds the DragenRNA_Settings and DragenRNA_Data sections. - -=cut - -sub add_rna_section { - my $self = shift; - - my @to_align = (); - my @ref_matches = keys %REFERENCE_MAPING; - my $distinct_configs = {}; - - foreach my $p ( $self->products() ) { - - my $r = $p->[$LIST_INDEX_REF]; - my $lib_type = $p->[$LIST_INDEX_LIBTYPE]; - - if ( can_do_alignment($r) && - (do_ref_rna_alignment_test($r) || do_libtype_rna_alignment_test($lib_type)) ) { - - my $match = first { $r =~ /$_/xms} @ref_matches; - if ($self->_can_add_sample($distinct_configs, $match)) { - push @to_align, [$p->[1], $REFERENCE_MAPING{$match}]; - } - } - } - - if (@to_align) { - $self->_add_line('[DragenRNA_Settings]'); - $self->_add_line(q(SoftwareVersion), $self->dragen_software_version); - $self->_add_line(qw(MapAlignOutFormat cram)); - $self->_add_line(q(KeepFastq), $self->keep_fastq ? 'TRUE' : 'FALSE'); - $self->_add_line(qw(RnaPipelineMode FullPipeline)); - $self->_add_line(); - - $self->_add_line('[DragenRNA_Data]'); - $self->_add_line(qw(Sample_ID ReferenceGenomeDir)); - $self->_add_samples(@to_align); - } - - return scalar @to_align; -} - __PACKAGE__->meta->make_immutable; 1; @@ -892,8 +928,6 @@ __END__ =item List::Util -=item Getopt::Long - =item Pod::Usage =item DateTime diff --git a/t/47-npg_samplesheet_novaseq_xseries.t b/t/47-npg_samplesheet_novaseq_xseries.t index ddc3ec98..b1229d6d 100644 --- a/t/47-npg_samplesheet_novaseq_xseries.t +++ b/t/47-npg_samplesheet_novaseq_xseries.t @@ -118,7 +118,7 @@ subtest 'create the generator object, test simple attributes' => sub { }; subtest 'generate a samplesheet' => sub { - plan tests => 6; + plan tests => 8; my $file_name = '47995_NVX1_A_ssbatch98292.csv'; my $compare_file_root = @@ -131,6 +131,9 @@ subtest 'generate a samplesheet' => sub { file_name => $file_name ); + is_deeply ($g->index_read_length(), [8,8], 'correct lengths of index reads'); + is_deeply ($g->read_length(), [151,151], 'correct lengths of reads'); + # The code creates a new samplesheet in the working directory. # This will be changed in future. $g->process(); From 85955368144c7290c7471fdfad8ecbe384f45524 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 18 Dec 2023 22:00:32 +0000 Subject: [PATCH 07/28] Improved documentation as advised by @jmtcsngr --- bin/npg_samplesheet_generator_NovaSeqXSeries | 6 ++++++ lib/npg/samplesheet/novaseq_xseries.pm | 12 +++++++----- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/bin/npg_samplesheet_generator_NovaSeqXSeries b/bin/npg_samplesheet_generator_NovaSeqXSeries index d759b0cc..3bf9ee5f 100755 --- a/bin/npg_samplesheet_generator_NovaSeqXSeries +++ b/bin/npg_samplesheet_generator_NovaSeqXSeries @@ -57,6 +57,12 @@ npg_samplesheet_generator_NovaSeqXSeries DRAGEN analysis can deal with a limited number of distinct configurations. Set this attribute if processing off-board. + C - + DRAGEN software version to use, optional + + C - + name of the samplesheet CSV file, optional + =head1 DESCRIPTION Generates a samplesheet for the NovaSeq Series X Illumina instrument and diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index 39faf030..27fb6853 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -201,7 +201,7 @@ has 'read_length' => ( 'is' => 'ro', 'lazy_build' => 1, 'required' => 0, - 'documentation' => 'An array containing the length of the forward and the ' . + 'documentation' => 'An array containing the length of the forward and ' . 'reverse read', ); sub _build_read_length { @@ -585,15 +585,17 @@ used when processing the sequencing data. Must adhere to the following requirements: - Must be same number of fields (delimited by semicolon) as sequencing and - indexing reads specified in RunInfo.xml or Reads section. + indexing reads specified in RunInfo.xml or 'Reads' section. -- Indexing reads are specified with I, sequencing reads are specified with - Y, UMI cycles are specified with U, and trimmed reads are specified with N. +- Indexing reads are specified with 'I', + sequencing reads are specified with 'Y', + UMI cycles are specified with 'U', + and trimmed reads are specified with 'N'. - The number of cycles specified for each read must equal the number of cycles specified for that read in the RunInfo.xml file. -- Only one Y or I sequence can be specified per read. +- Only one 'Y' or 'I' sequence can be specified per read. =cut From 6ad9feb2e0daf0e637c9740746a799ac31e60947 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 15 Dec 2023 18:32:14 +0000 Subject: [PATCH 08/28] Added ability to set path for NovaSeqX ssheet. Created a parent class for two existing samplesheet generators. Moved common methods to this class. Through this inheritance the NovaSeqX samplesheet generator gets a standard method for setting a configurable path for a samplesheet. --- MANIFEST | 1 + lib/npg/samplesheet.pm | 124 +--------- lib/npg/samplesheet/base.pm | 260 +++++++++++++++++++++ lib/npg/samplesheet/novaseq_xseries.pm | 300 +++++++++---------------- t/47-npg_samplesheet_novaseq_xseries.t | 45 ++-- 5 files changed, 408 insertions(+), 322 deletions(-) create mode 100755 lib/npg/samplesheet/base.pm diff --git a/MANIFEST b/MANIFEST index ba18d2b8..9a0e6ba4 100644 --- a/MANIFEST +++ b/MANIFEST @@ -161,6 +161,7 @@ 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 diff --git a/lib/npg/samplesheet.pm b/lib/npg/samplesheet.pm index 1c342174..ea70c816 100755 --- a/lib/npg/samplesheet.pm +++ b/lib/npg/samplesheet.pm @@ -2,22 +2,16 @@ package npg::samplesheet; use Moose; use namespace::autoclean; -use Class::Load qw(load_class); use Template; -use Carp qw(carp croak confess); +use Carp; use List::MoreUtils qw(any uniq); use URI::Escape qw(uri_escape_utf8); use Readonly; use open q(:encoding(UTF8)); -use npg_tracking::Schema; -use st::api::lims; use st::api::lims::samplesheet; -use npg_tracking::util::config qw(get_config_staging_areas); -use npg_tracking::util::abs_path qw(abs_path); -use WTSI::DNAP::Warehouse::Schema; -with 'npg_tracking::glossary::run'; +extends 'npg::samplesheet::base'; our $VERSION = '0'; @@ -60,10 +54,7 @@ still retained in the relevant custom fields. =cut -my$config=get_config_staging_areas(); -Readonly::Scalar my $SAMPLESHEET_PATH => $config->{'samplesheets'}||q(samplesheets/); -Readonly::Scalar my $MIN_COLUMN_NUM => 3; -Readonly::Scalar my $DEFAULT_LIMS_DRIVER_TYPE => 'ml_warehouse'; +Readonly::Scalar my $MIN_COLUMN_NUM => 3; ################################################################## ####################### Public attributes ######################## @@ -84,26 +75,7 @@ sub _build_id_run { if($self->has_tracking_run()){ return $self->run()->id_run(); } - confess 'id_run or a run is required'; -} - -=head2 samplesheet_path - -An optional attribute. - -=cut - -has 'samplesheet_path' => ( - 'isa' => 'Str', - 'is' => 'ro', - 'lazy_build' => 1, -); -sub _build_samplesheet_path { - if($ENV{dev} and not $ENV{dev}=~/live/smix){ - my ($suffix) = $ENV{dev}=~/(\w+)/smix; - return $SAMPLESHEET_PATH . $suffix . q(/); - } - return $SAMPLESHEET_PATH; + croak 'id_run or a run is required'; } =head2 extend @@ -139,88 +111,6 @@ An attribute, a path to the root of the reference repository. has 'repository' => ( 'isa' => 'Str', 'is' => 'ro' ); -=head2 npg_tracking_schema - -An attribute, DBIx Schema object for the tracking database. - -=cut - -has 'npg_tracking_schema' => ( - 'isa' => 'npg_tracking::Schema', - 'is' => 'ro', - 'lazy_build' => 1, -); -sub _build_npg_tracking_schema { - my ($self) = @_; - my$s = $self->has_tracking_run() ? - $self->run()->result_source()->schema() : - npg_tracking::Schema->connect(); - return $s -} - -=head2 mlwh_schema - -DBIx schema class for ml_warehouse access. - -=cut - -has 'mlwh_schema' => ( - 'isa' => 'WTSI::DNAP::Warehouse::Schema', - 'is' => 'ro', - 'required' => 0, - 'lazy_build' => 1, -); -sub _build_mlwh_schema { - return WTSI::DNAP::Warehouse::Schema->connect(); -} - -=head2 run - -An attribute, DBIx object for a row in the run table of the tracking database. - -=cut - -has 'run' => ( - 'isa' => 'npg_tracking::Schema::Result::Run', - 'is' => 'ro', - 'predicate' => 'has_tracking_run', - 'lazy_build' => 1, -); -sub _build_run { - my $self=shift; - return $self->npg_tracking_schema->resultset(q(Run))->find($self->id_run); -} - -=head2 lims - -An attribute, an array of st::api::lims type objects. - -To generate a samplesheet for the whole run, provide an array of -at::api::lims objects for all lanes of the run. - -This attribute should normally be provided by the caller via the -constuctor. If the attribute is not provided, it is built automatically, -using the ml_warehouse lims driver. - -=cut - -has 'lims' => ( - 'isa' => 'ArrayRef[st::api::lims]', - 'is' => 'ro', - 'lazy_build' => 1, -); -sub _build_lims { - my $self=shift; - - my $run_lims = st::api::lims->new( - driver_type => $DEFAULT_LIMS_DRIVER_TYPE, - id_flowcell_lims => $self->run->batch_id, - mlwh_schema => $self->mlwh_schema - ); - - return [$run_lims->children()]; -}; - =head2 output An attribute, a file path or handle or a scalar reference. @@ -595,8 +485,6 @@ __END__ =item namespace::autoclean -=item Class::Load - =item Template =item Readonly @@ -609,8 +497,6 @@ __END__ =item open -=item WTSI::DNAP::Warehouse::Schema - =back =head1 INCOMPATIBILITIES @@ -623,7 +509,7 @@ David K. Jackson Edavid.jackson@sanger.ac.ukE =head1 LICENSE AND COPYRIGHT -Copyright (C) 2019,2020, 2023 Genome Research Ltd. +Copyright (C) 2019, 2020, 2023 Genome Research Ltd. This file is part of NPG. diff --git a/lib/npg/samplesheet/base.pm b/lib/npg/samplesheet/base.pm new file mode 100755 index 00000000..834ee073 --- /dev/null +++ b/lib/npg/samplesheet/base.pm @@ -0,0 +1,260 @@ +package npg::samplesheet::base; + +use Moose; +use namespace::autoclean; +use Carp; +use Readonly; +use MooseX::Getopt::Meta::Attribute::Trait::NoGetopt; + +use npg_tracking::Schema; +use st::api::lims; +use npg_tracking::util::config qw(get_config_staging_areas); +use WTSI::DNAP::Warehouse::Schema; + +with 'npg_tracking::glossary::run'; + +our $VERSION = '0'; + +=head1 NAME + +npg::samplesheet::base + +=head1 SYNOPSIS + +=head1 DESCRIPTION + +A parent class for samplesheet generator. Provides common attributes. + +=head1 DIAGNOSTICS + +=head1 CONFIGURATION AND ENVIRONMENT + +=cut + +my$config=get_config_staging_areas(); +Readonly::Scalar my $SAMPLESHEET_PATH => $config->{'samplesheets'}||q(samplesheets/); +Readonly::Scalar my $LIMS_DRIVER_TYPE => 'ml_warehouse'; + +=head1 SUBROUTINES/METHODS + +=cut + +=head2 samplesheet_path + +A directory where the samplesheet will be created, an optional attribute. + +=cut + +has 'samplesheet_path' => ( + 'isa' => 'Str', + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build_samplesheet_path { + if($ENV{dev} and not $ENV{dev}=~/live/smix){ + my ($suffix) = $ENV{dev}=~/(\w+)/smix; + return $SAMPLESHEET_PATH . $suffix . q(/); + } + return $SAMPLESHEET_PATH; +} + + +=head2 id_run + +Run ID, an optional attribute. + +=cut + +has '+id_run' => ( + 'required' => 0, +); + + +=head2 batch_id + +LIMS batch ID, an optional attribute. If not set, either C or +C attribute should be set. + +=cut + +has 'batch_id' => ( + 'isa' => 'Str|Int', + 'is' => 'ro', + 'lazy_build' => 1, + 'required' => 0, +); +sub _build_batch_id { + my $self = shift; + if (!$self->id_run) { + croak 'Run ID is not supplied, cannot get LIMS batch ID'; + } + my $batch_id = $self->run()->batch_id(); + if (!defined $batch_id) { + croak 'Batch ID is not set in the database record for run ' . $self->id_run; + } + + return $batch_id; +} + + +=head2 npg_tracking_schema + +An attribute, DBIx Schema object for the tracking database. + +=cut + +has 'npg_tracking_schema' => ( + 'isa' => 'npg_tracking::Schema', + 'traits' => [ 'NoGetopt' ], + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build_npg_tracking_schema { + my ($self) = @_; + my$s = $self->has_tracking_run() ? + $self->run()->result_source()->schema() : + npg_tracking::Schema->connect(); + return $s +} + +=head2 mlwh_schema + +DBIx schema class for ml_warehouse access. + +=cut + +has 'mlwh_schema' => ( + 'isa' => 'WTSI::DNAP::Warehouse::Schema', + 'traits' => [ 'NoGetopt' ], + 'is' => 'ro', + 'required' => 0, + 'lazy_build' => 1, +); +sub _build_mlwh_schema { + return WTSI::DNAP::Warehouse::Schema->connect(); +} + + +=head2 run + +An attribute, DBIx object for a row in the run table of the tracking database. + +=cut + +has 'run' => ( + 'isa' => 'npg_tracking::Schema::Result::Run', + 'traits' => [ 'NoGetopt' ], + 'is' => 'ro', + 'predicate' => 'has_tracking_run', + 'lazy_build' => 1, +); +sub _build_run { + my $self=shift; + + if (!$self->id_run) { + croak 'Run ID is not available, cannot retrieve run database record'; + } + my $run = $self->npg_tracking_schema->resultset(q(Run))->find($self->id_run); + if (!$run) { + croak 'The database record for run ' . $self->id_run . ' does not exist'; + } + + return $run; +} + + +=head2 lims + +An attribute, an array of st::api::lims type objects. + +To generate a samplesheet for the whole run, provide an array of +at::api::lims objects for all lanes of the run. + +This attribute should normally be provided by the caller via the +constuctor. If the attribute is not provided, it is built automatically, +using the ml_warehouse lims driver. + +=cut + +has 'lims' => ( + 'isa' => 'ArrayRef[st::api::lims]', + 'traits' => [ 'NoGetopt' ], + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build_lims { + my $self=shift; + + my $run_lims = st::api::lims->new( + driver_type => $LIMS_DRIVER_TYPE, + id_flowcell_lims => $self->batch_id, + mlwh_schema => $self->mlwh_schema + ); + + return [$run_lims->children()]; +}; + +__PACKAGE__->meta->make_immutable; + +1; + +__END__ + + +=head1 DEPENDENCIES + +=over + +=item Moose + +=item namespace::autoclean + +=item Readonly + +=item Carp + +=item MooseX::Getopt::Meta::Attribute::Trait::NoGetopt + +=item WTSI::DNAP::Warehouse::Schema + +=item npg_tracking::Schema + +=item st::api::lims + +=item npg_tracking::util::config + +=item npg_tracking::glossary::run + +=back + +=head1 INCOMPATIBILITIES + +=head1 BUGS AND LIMITATIONS + +=head1 AUTHOR + +David K. Jackson Edavid.jackson@sanger.ac.ukE + +Marina Gourtovaia Emg8@sanger.ac.ukE + +=head1 LICENSE AND COPYRIGHT + +Copyright (C) 2019, 2020, 2023 Genome Research Ltd. + +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 . + +=cut + diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index 27fb6853..c4addb20 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -8,17 +8,13 @@ use Carp; use Text::CSV; use List::MoreUtils qw(any none uniq); use List::Util qw(first max); -use Pod::Usage; use DateTime; use Data::UUID; -use st::api::lims; -use npg_tracking::Schema; -use npg_tracking::util::types; -use WTSI::DNAP::Warehouse::Schema; +use st::api::lims::samplesheet; -with qw / MooseX::Getopt - npg_tracking::glossary::run /; +extends 'npg::samplesheet::base'; +with 'MooseX::Getopt'; our $VERSION = '0'; @@ -38,9 +34,8 @@ Readonly::Hash my %REFERENCE_MAPING => ( 'Homo_sapiens' => 'hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2' ); -# DRAGEN can process a limited number of distinct configurations. -# For on-board analysis it's 4. Readonly::Scalar my $DRAGEN_MAX_NUMBER_OF_CONFIGS => 4; +Readonly::Scalar my $END_OF_LINE => qq[\n]; =head1 NAME @@ -116,49 +111,90 @@ sub _build_dragen_software_version { }; -=head2 id_run +has '+samplesheet_path' => ( + 'documentation' => 'A directory where the samplesheet will be created, ' . + 'optional', +); + + +=head2 file_name -NPG run ID, an optional attribute. If supplied, the record for this run -should exists in the run tracking database. +CSV file name to write the samplesheet data to. =cut -has '+id_run' => ( - 'required' => 0, - 'documentation' => 'NPG run ID, optional; if supplied, the record for this '. - 'run should exists in the run tracking database', +has 'file_name' => ( + 'isa' => 'Str', + 'is' => 'ro', + 'lazy_build' => 1, + 'required' => 0, + 'documentation' => 'CSV file name to write the samplesheet data to, ' . + 'optional', ); +sub _build_file_name { + my $self = shift; + my $file_name; + if ($self->has_id_run) { + $file_name = join q[_], + $self->run_name, + q[ssbatch] . $self->batch_id; + } else { + $file_name = $self->run_name; + } -=head2 batch_id + my $date = DateTime->now()->strftime('%y%m%d'); # 230602 for 2 June 2023 + $file_name = sprintf '%s_%s.csv', $date, $file_name; + + return $file_name; +} + + +=head2 output -LIMS batch ID, an optional attribute. If not set, the C attribute -should be set. +A full path of the samplesheet file. If not supplied, is built using the +values of C and C attributes. + +If the C attribute is set to an empty string, the current +working directory is assumed. + +Do not remove this attribute or change its name in order to be compliant with +the samplesheet daemon C. =cut -has 'batch_id' => ( - 'isa' => 'Str|Int', - 'is' => 'ro', +has 'output' => ( + 'isa' => 'Str', + 'is' => 'ro', 'lazy_build' => 1, - 'required' => 0, - 'documentation' => 'LIMS batch identifier, optional. If not set, will be ' . - 'retrieved from the tracking database record for the run', + 'isa' => 'Str', + 'documentation' => 'A path of the samplesheet file, optional', ); -sub _build_batch_id { +sub _build_output { my $self = shift; - if (!$self->has_id_run) { - croak 'Run ID is not supplied, cannot get LIMS batch ID'; - } - my $batch_id = $self->run()->batch_id(); - if (!defined $batch_id) { - croak 'Batch ID is not set in the database record for run ' . $self->id_run; + + my $dir = $self->samplesheet_path(); + my $path = $self->file_name; + if ($dir) { + $dir =~ s{/\Z}{}xms; # Trim trailing slash if present. + $path = join q[/], $dir, $path; } - return $batch_id; + return $path; } +has '+id_run' => ( + 'documentation' => 'NPG run ID, optional; if supplied, the record for this '. + 'run should exists in the run tracking database', +); + + +has '+batch_id' => ( + 'documentation' => 'LIMS batch identifier, optional. If not set, will be ' . + 'retrieved from the tracking database record for the run', +); + =head2 index_read_length An array containing the length of the first and the second (if applicable) @@ -175,7 +211,7 @@ has 'index_read_length' => ( 'lazy_build' => 1, 'required' => 0, 'documentation' => 'An array containing the length of the first and the ' . - 'second (if applicable) indexing read..', + 'second (if applicable) indexing read.', ); sub _build_index_read_length { my $self = shift; @@ -273,96 +309,6 @@ has 'dragen_max_number_of_configs' => ( ); -=head2 npg_tracking_schema - -DBIx Schema object for the tracking database. - -=cut - -has 'npg_tracking_schema' => ( - 'isa' => 'npg_tracking::Schema', - 'is' => 'ro', - 'lazy_build' => 1, - 'traits' => [ 'NoGetopt' ], -); -sub _build_npg_tracking_schema { - return npg_tracking::Schema->connect(); -} - - -=head2 mlwh_schema - -DBIx Schema object for the mlwh database. - -=cut - -has 'mlwh_schema' => ( - 'isa' => 'WTSI::DNAP::Warehouse::Schema', - 'is' => 'ro', - 'lazy_build' => 1, - 'traits' => [ 'NoGetopt' ], -); -sub _build_mlwh_schema { - return WTSI::DNAP::Warehouse::Schema->connect(); -} - - -=head2 run - -DBIx object for a row in the run table of the tracking database. - -=cut - -has 'run' => ( - 'isa' => 'npg_tracking::Schema::Result::Run', - 'is' => 'ro', - 'predicate' => 'has_tracking_run', - 'lazy_build' => 1, - 'traits' => [ 'NoGetopt' ], -); -sub _build_run { - my $self=shift; - - if (!$self->has_id_run) { - croak 'Run ID is not supplied, cannot retrieve run database record'; - } - my $run = $self->npg_tracking_schema->resultset(q(Run))->find($self->id_run); - if (!$run) { - croak 'The database record for run ' . $self->id_run . ' does not exist'; - } - if ($run->instrument_format()->model() !~ /NovaSeqX/smx) { - croak 'Instrument model is not NovaSeq X Series'; - } - - return $run; -} - - -=head2 lims - -An attribute, an array of C type objects. - -If the attribute is not provided, it is built automatically. -c driver is used to access LIMS data. - -=cut - -has 'lims' => ( - 'isa' => 'ArrayRef[st::api::lims]', - 'is' => 'ro', - 'lazy_build' => 1, - 'traits' => [ 'NoGetopt' ], -); -sub _build_lims { - my $self=shift; - return [st::api::lims->new( - id_flowcell_lims => $self->batch_id, - driver_type => q[ml_warehouse], - mlwh_schema => $self->mlwh_schema - )->children()]; -} - - =head2 run_name =cut @@ -378,7 +324,10 @@ sub _build_run_name { my $self = shift; my $run_name; - if ($self->has_id_run()) { + if ($self->id_run()) { + if ($self->run->instrument_format()->model() !~ /NovaSeqX/smx) { + croak 'Instrument model is not NovaSeq X Series'; + } # Embed instrument's Sanger network name and slot $run_name = sprintf '%s_%s_%s', $self->id_run, $self->run->instrument->name, $self->get_instrument_side; @@ -394,36 +343,6 @@ sub _build_run_name { } -=head2 file_name - -=cut - -has 'file_name' => ( - 'isa' => 'Str', - 'is' => 'ro', - 'lazy_build' => 1, - 'required' => 0, - 'documentation' => 'CSV file name or path to write samplesheet data to', -); -sub _build_file_name { - my $self = shift; - - my $file_name; - if ($self->has_id_run) { - $file_name = join q[_], - $self->run_name, - q[ssbatch] . $self->batch_id; - } else { - $file_name = $self->run_name; - } - - my $date = DateTime->now()->strftime('%y%m%d'); # 230602 for 2 June 2023 - $file_name = sprintf '%s_%s.csv', $date, $file_name; - - return $file_name; -} - - =head2 products A list of products as given by LIMS, a read-only accessor. @@ -471,6 +390,9 @@ sub _build__products { Generates a samplesheet and saves it to a file. +Do not remove this method or change its name in order to stay compliant +with samplesheet daemon C. + =cut sub process { @@ -508,30 +430,7 @@ sub process { carp 'Too many BCLConvert configurations, cannot run any DRAGEN analysis'; } - - my $csv = Text::CSV->new({ - eol => qq[\n], - sep_char => q[,], - }); - - my $max_num_columns = max map { scalar @{$_} } @{$self->_all_lines}; - - my $file_name = $self->file_name; - ## no critic (InputOutput::RequireBriefOpen) - open my $fh, q[>], $file_name - or croak "Failed to open $file_name for writing"; - - for my $line (@{$self->_all_lines}) { - my @columns = @{$line}; - # Pad the row. - while (scalar @columns < $max_num_columns) { - push @columns, q[]; - } - $csv->print($fh, \@columns); - } - - close $fh or carp "Problems closing $file_name"; - ## use critic + $self->_generate_output(); return; } @@ -898,6 +797,37 @@ sub _can_add_sample { return 1; } + +sub _generate_output { + my $self = shift; + + my $csv = Text::CSV->new({ + eol => $END_OF_LINE, + sep_char => $st::api::lims::samplesheet::SAMPLESHEET_RECORD_SEPARATOR + }); + + my $max_num_columns = max map { scalar @{$_} } @{$self->_all_lines}; + + my $file_path = $self->output; + ## no critic (InputOutput::RequireBriefOpen) + open my $fh, q[>], $file_path + or croak "Failed to open $file_path for writing"; + + for my $line (@{$self->_all_lines}) { + my @columns = @{$line}; + # Pad the row. + while (scalar @columns < $max_num_columns) { + push @columns, q[]; + } + $csv->print($fh, \@columns); + } + + close $fh or carp "Problems closing $file_path"; + ## use critic + + return; +} + __PACKAGE__->meta->make_immutable; 1; @@ -930,20 +860,10 @@ __END__ =item List::Util -=item Pod::Usage - =item DateTime =item Data::UUID -=item st::api::lims - -=item npg_tracking::Schema - -=item npg_tracking::util::types - -=item WTSI::DNAP::Warehouse::Schema - =back =head1 BUGS AND LIMITATIONS @@ -956,7 +876,7 @@ Marina Gourtovaia Emg8@sanger.ac.ukE =head1 LICENSE AND COPYRIGHT -Copyright (C) 2023 Genome Research Ltd +Copyright (C) 2023 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 diff --git a/t/47-npg_samplesheet_novaseq_xseries.t b/t/47-npg_samplesheet_novaseq_xseries.t index b1229d6d..69768d99 100644 --- a/t/47-npg_samplesheet_novaseq_xseries.t +++ b/t/47-npg_samplesheet_novaseq_xseries.t @@ -5,11 +5,14 @@ use Test::Exception; use Moose::Meta::Class; use DateTime; use Perl6::Slurp; +use File::Temp qw/ tempdir /; use npg_testing::db; use_ok('npg::samplesheet::novaseq_xseries'); +my $dir = tempdir(UNLINK => 1); + my $class = Moose::Meta::Class->create_anon_class(roles=>[qw/npg_testing::db/]); my $schema_tracking = $class->new_object({})->create_test_db( @@ -23,7 +26,7 @@ my $schema_wh = $class->new_object({})->create_test_db( my $date = DateTime->now()->strftime('%y%m%d'); subtest 'create the generator object, test simple attributes' => sub { - plan tests => 14; + plan tests => 16; my $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, @@ -102,9 +105,20 @@ subtest 'create the generator object, test simple attributes' => sub { npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, id_run => 47446, + samplesheet_path => "$dir/one/" ); - is ($g->file_name, "${date}_47446_NVX1_B_ssbatch99888.csv", + my $file_name = $g->file_name; + is ($file_name, "${date}_47446_NVX1_B_ssbatch99888.csv", 'correct file name is generated'); + is ($g->output, "$dir/one/$file_name", 'correct output path is generated'); + + $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + id_run => 47446, + samplesheet_path => q[] + ); + is ($g->output, $file_name, 'correct output path is generated'); $run_row->update({id_instrument_format => 10, id_instrument => 68}); $g = npg::samplesheet::novaseq_xseries->new( @@ -118,7 +132,7 @@ subtest 'create the generator object, test simple attributes' => sub { }; subtest 'generate a samplesheet' => sub { - plan tests => 8; + plan tests => 9; my $file_name = '47995_NVX1_A_ssbatch98292.csv'; my $compare_file_root = @@ -128,50 +142,55 @@ subtest 'generate a samplesheet' => sub { npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, id_run => 47995, - file_name => $file_name + file_name => $file_name, + samplesheet_path => $dir, ); is_deeply ($g->index_read_length(), [8,8], 'correct lengths of index reads'); is_deeply ($g->read_length(), [151,151], 'correct lengths of reads'); + my $path = $g->output(); + is ($path, "$dir/$file_name", 'correct samplesheet path'); # The code creates a new samplesheet in the working directory. # This will be changed in future. $g->process(); - ok (-e $file_name, 'the samplesheet file exists'); + ok (-e $path, 'the samplesheet file exists'); my $compare_file = $compare_file_root . '.csv'; - is (slurp($file_name), slurp($compare_file), + is (slurp($path), slurp($compare_file), 'the samplesheet is generated correctly'); - unlink $file_name; + unlink $path; $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, id_run => 47995, file_name => $file_name, + samplesheet_path => $dir, align => 1, keep_fastq => 1 ); $g->process(); - ok (-e $file_name, 'the samplesheet file exists'); + ok (-e $path, 'the samplesheet file exists'); $compare_file = $compare_file_root . '_align.csv'; - is (slurp($file_name), slurp($compare_file), + is (slurp($path), slurp($compare_file), 'the samplesheet is generated correctly'); - unlink $file_name; + unlink $path; $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, id_run => 47995, file_name => $file_name, + samplesheet_path => $dir, align => 1, varcall => 'AllVariantCallers' ); $g->process(); - ok (-e $file_name, 'the samplesheet file exists'); + ok (-e $path, 'the samplesheet file exists'); $compare_file = $compare_file_root . '_varcall.csv'; - is (slurp($file_name), slurp($compare_file), + is (slurp($path), slurp($compare_file), 'the samplesheet is generated correctly'); - unlink $file_name; + unlink $path; }; 1; From 5aa50059f80334538e18e90eb146dfddf9396a98 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 18 Dec 2023 15:30:35 +0000 Subject: [PATCH 09/28] Simplifies the default samplesheet path. An option to read the value from the configuration file is not used. --- lib/npg/samplesheet/base.pm | 15 ++------------- t/.npg/npg_tracking | 1 - t/47-samplesheet.t | 13 +++---------- 3 files changed, 5 insertions(+), 24 deletions(-) diff --git a/lib/npg/samplesheet/base.pm b/lib/npg/samplesheet/base.pm index 834ee073..cdef7dce 100755 --- a/lib/npg/samplesheet/base.pm +++ b/lib/npg/samplesheet/base.pm @@ -8,7 +8,6 @@ use MooseX::Getopt::Meta::Attribute::Trait::NoGetopt; use npg_tracking::Schema; use st::api::lims; -use npg_tracking::util::config qw(get_config_staging_areas); use WTSI::DNAP::Warehouse::Schema; with 'npg_tracking::glossary::run'; @@ -31,8 +30,7 @@ A parent class for samplesheet generator. Provides common attributes. =cut -my$config=get_config_staging_areas(); -Readonly::Scalar my $SAMPLESHEET_PATH => $config->{'samplesheets'}||q(samplesheets/); +Readonly::Scalar my $SAMPLESHEET_PATH => 'samplesheets/'; Readonly::Scalar my $LIMS_DRIVER_TYPE => 'ml_warehouse'; =head1 SUBROUTINES/METHODS @@ -48,15 +46,8 @@ A directory where the samplesheet will be created, an optional attribute. has 'samplesheet_path' => ( 'isa' => 'Str', 'is' => 'ro', - 'lazy_build' => 1, + 'default' => $SAMPLESHEET_PATH, ); -sub _build_samplesheet_path { - if($ENV{dev} and not $ENV{dev}=~/live/smix){ - my ($suffix) = $ENV{dev}=~/(\w+)/smix; - return $SAMPLESHEET_PATH . $suffix . q(/); - } - return $SAMPLESHEET_PATH; -} =head2 id_run @@ -221,8 +212,6 @@ __END__ =item st::api::lims -=item npg_tracking::util::config - =item npg_tracking::glossary::run =back diff --git a/t/.npg/npg_tracking b/t/.npg/npg_tracking index c16606b7..5a7b7c0d 100644 --- a/t/.npg/npg_tracking +++ b/t/.npg/npg_tracking @@ -3,7 +3,6 @@ my $VAR1 = { 'staging_areas' => { 'indexes' => [18 .. 32, 34 .. 47, 49 .. 55], 'prefix' => '/nfs/sf', - 'samplesheets' => '/nfs/sf49/ILorHSorMS_sf49/samplesheets/' }, 'staging_areas2webservers' => { 'gs01' => {'npg_tracking' => 'http://gso1.san.ac.uk:678', diff --git a/t/47-samplesheet.t b/t/47-samplesheet.t index f8753b25..aca2eaf4 100644 --- a/t/47-samplesheet.t +++ b/t/47-samplesheet.t @@ -9,8 +9,6 @@ use File::Path qw/make_path/; use Moose::Meta::Class; use t::dbic_util; -local $ENV{'dev'} = q(wibble); -local $ENV{'HOME'} = q(t/); use_ok('npg::samplesheet'); use_ok('st::api::lims'); @@ -22,8 +20,6 @@ my $mlwh_schema = $class->new_object({})->create_test_db( q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh_samplesheet] ); -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q(t/data/samplesheet); - my $dir = tempdir( CLEANUP => 1 ); subtest 'simple tests for the default driver' => sub { @@ -51,22 +47,19 @@ subtest 'object creation' => sub { lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } 'samplesheet object - no output provided'; - cmp_ok($ss->output, 'eq', - '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS0001309-300.csv', + cmp_ok($ss->output, 'eq', 'samplesheets/MS0001309-300.csv', 'default output location (with zeroes trimmed appropriately)'); lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946); } 'samplesheet object - no output provided'; - cmp_ok($ss->output, 'eq', - '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/000000000-A0616.csv', + cmp_ok($ss->output, 'eq', 'samplesheets/000000000-A0616.csv', 'default output location'); lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } 'samplesheet object - no output provided'; my $orig_flowcell_id = $ss->run->flowcell_id; $ss->run->flowcell_id(q(MS2000132-500V2)); - cmp_ok($ss->output, 'eq', - '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS2000132-500V2.csv', + cmp_ok($ss->output, 'eq', 'samplesheets/MS2000132-500V2.csv', 'default output location copes with V2 MiSeq cartirdges/reagent kits'); }; From 8a0efa360eff2285a6e749f0384acfc8351a8b79 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 20 Dec 2023 13:59:22 +0000 Subject: [PATCH 10/28] Small improvements following the code review --- lib/npg/samplesheet/base.pm | 2 +- lib/npg/samplesheet/novaseq_xseries.pm | 7 ++++--- t/47-npg_samplesheet_novaseq_xseries.t | 12 ++++++++++-- 3 files changed, 15 insertions(+), 6 deletions(-) diff --git a/lib/npg/samplesheet/base.pm b/lib/npg/samplesheet/base.pm index cdef7dce..866918c7 100755 --- a/lib/npg/samplesheet/base.pm +++ b/lib/npg/samplesheet/base.pm @@ -210,7 +210,7 @@ __END__ =item npg_tracking::Schema -=item st::api::lims +=item st::api::lims =item npg_tracking::glossary::run diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index c4addb20..cff01692 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -143,7 +143,7 @@ sub _build_file_name { $file_name = $self->run_name; } - my $date = DateTime->now()->strftime('%y%m%d'); # 230602 for 2 June 2023 + my $date = DateTime->now()->strftime('%y%m%d'); # 230602 for 2 June 2023 $file_name = sprintf '%s_%s.csv', $date, $file_name; return $file_name; @@ -176,7 +176,7 @@ sub _build_output { my $dir = $self->samplesheet_path(); my $path = $self->file_name; if ($dir) { - $dir =~ s{/\Z}{}xms; # Trim trailing slash if present. + $dir =~ s{[/]+\Z}{}xms; # Trim trailing slash if present. $path = join q[/], $dir, $path; } @@ -326,7 +326,8 @@ sub _build_run_name { my $run_name; if ($self->id_run()) { if ($self->run->instrument_format()->model() !~ /NovaSeqX/smx) { - croak 'Instrument model is not NovaSeq X Series'; + croak 'Instrument is not registered as NovaSeq X Series ' . + 'in the tracking database'; } # Embed instrument's Sanger network name and slot $run_name = sprintf '%s_%s_%s', $self->id_run, diff --git a/t/47-npg_samplesheet_novaseq_xseries.t b/t/47-npg_samplesheet_novaseq_xseries.t index 69768d99..9778f372 100644 --- a/t/47-npg_samplesheet_novaseq_xseries.t +++ b/t/47-npg_samplesheet_novaseq_xseries.t @@ -26,7 +26,7 @@ my $schema_wh = $class->new_object({})->create_test_db( my $date = DateTime->now()->strftime('%y%m%d'); subtest 'create the generator object, test simple attributes' => sub { - plan tests => 16; + plan tests => 17; my $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, @@ -112,6 +112,14 @@ subtest 'create the generator object, test simple attributes' => sub { 'correct file name is generated'); is ($g->output, "$dir/one/$file_name", 'correct output path is generated'); + $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + id_run => 47446, + samplesheet_path => "$dir/one///" + ); + is ($g->output, "$dir/one/$file_name", 'correct output path is generated'); + $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, @@ -127,7 +135,7 @@ subtest 'create the generator object, test simple attributes' => sub { id_run => 47446, ); throws_ok { $g->file_name } - qr/Instrument model is not NovaSeq X Series/, + qr/Instrument is not registered as NovaSeq X Series/, 'error when the run is registered on the wrong instrument model'; }; From daeb7d9ba936140fe7d3d293944bebf8e1a87318 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 18 Dec 2023 17:37:19 +0000 Subject: [PATCH 11/28] Samplesheet daemon extension for NovaSeqX --- lib/npg/samplesheet/auto.pm | 43 +++++++++++++++++++++++--- lib/npg/samplesheet/novaseq_xseries.pm | 4 ++- t/47-npg_samplesheet_auto.t | 36 ++++++++++++++++++--- 3 files changed, 72 insertions(+), 11 deletions(-) diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index 267eaf17..ce007663 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -8,11 +8,13 @@ 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); @@ -20,6 +22,10 @@ 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, id_run => $id_run, + mlwh_schema => $self->mlwh_schema, + align => 1, keep_fastq => 1, + varcall => q(AllVariantCallers) + ); + } + 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; diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index cff01692..18694210 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/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'; } diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t index 813e2baa..9d6a6d31 100644 --- a/t/47-npg_samplesheet_auto.t +++ b/t/47-npg_samplesheet_auto.t @@ -1,17 +1,20 @@ use strict; use warnings; -use Test::More tests => 12; +use Test::More tests => 14; use Test::Exception; use File::Temp qw/ tempdir /; use Moose::Meta::Class; use Log::Log4perl qw(:easy); +use File::chdir; 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; @@ -27,7 +30,7 @@ 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'; } { @@ -35,7 +38,7 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema]); '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 +69,27 @@ 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/$glob"; + is (@files, 1, 'one NovaSeqX samplesheet file is generated'); +} + 1; From 5755c97e882502232f6a60dfb9037ba0c7ed73a0 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 19 Dec 2023 08:12:03 +0000 Subject: [PATCH 12/28] Added a script to generate samplesheets for pending NovaSeqX runs --- MANIFEST | 2 + bin/npg_samplesheet4NovaSeqX | 98 ++++++++++++++++++++ bin/npg_samplesheet_generator_NovaSeqXSeries | 4 +- 3 files changed, 102 insertions(+), 2 deletions(-) create mode 100755 bin/npg_samplesheet4NovaSeqX diff --git a/MANIFEST b/MANIFEST index 9a0e6ba4..2822beba 100644 --- a/MANIFEST +++ b/MANIFEST @@ -3,6 +3,8 @@ bin/illumina_instruments_uptime bin/npg_daemon_control bin/npg_move_runfolder bin/npg_samplesheet4MiSeq +bin/npg_samplesheet4NovaSeqX +bin/npg_samplesheet_generator_NovaSeqXSeries bin/npg_status_save bin/staging_area_monitor bin/npg_deletable_dr_runs diff --git a/bin/npg_samplesheet4NovaSeqX b/bin/npg_samplesheet4NovaSeqX new file mode 100755 index 00000000..1123d4c2 --- /dev/null +++ b/bin/npg_samplesheet4NovaSeqX @@ -0,0 +1,98 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use FindBin qw($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 Emg8@sanger.ac.ukE + +=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 . + +=cut diff --git a/bin/npg_samplesheet_generator_NovaSeqXSeries b/bin/npg_samplesheet_generator_NovaSeqXSeries index 3bf9ee5f..ddd769bd 100755 --- a/bin/npg_samplesheet_generator_NovaSeqXSeries +++ b/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 From 7337e997b1282a9db3bc1a1c1c0ac273e46c2504 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 19 Dec 2023 08:46:40 +0000 Subject: [PATCH 13/28] Supressed variant calling. Added a test to test the correctness of passing the option to teh samplesheet generator. --- lib/npg/samplesheet/auto.pm | 3 +-- t/47-npg_samplesheet_auto.t | 7 ++++++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index ce007663..e41d05a6 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -156,8 +156,7 @@ sub process { $ss = npg::samplesheet::novaseq_xseries->new( run => $r, id_run => $id_run, mlwh_schema => $self->mlwh_schema, - align => 1, keep_fastq => 1, - varcall => q(AllVariantCallers) + align => 1, keep_fastq => 1 ); } diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t index 9d6a6d31..ca8814ca 100644 --- a/t/47-npg_samplesheet_auto.t +++ b/t/47-npg_samplesheet_auto.t @@ -1,11 +1,12 @@ use strict; use warnings; -use Test::More tests => 14; +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'); @@ -90,6 +91,10 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema], my $glob = q[*_47995_NVX1_A_ssbatch98292.csv]; my @files = glob "$dir/samplesheets/$glob"; is (@files, 1, 'one NovaSeqX samplesheet file is generated'); + my $compare_file = 't/data/samplesheet/dragen/' . + '231206_47995_NVX1_A_ssbatch98292_align.csv'; + is (slurp($files[0]), slurp($compare_file), + 'the NovaSeqX samplesheet is generated correctly'); } 1; From 58ce63dd49c22869337da4c335ac945dae4605a8 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 19 Dec 2023 09:04:18 +0000 Subject: [PATCH 14/28] Supressed keeping interim fastq files --- lib/npg/samplesheet/auto.pm | 8 +++++--- t/47-npg_samplesheet_auto.t | 4 +++- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index e41d05a6..f014b9ea 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -150,13 +150,15 @@ sub process { my $ss; if ($self->instrument_format eq $MISEQ_INSTRUMENT_FORMAT) { $ss = npg::samplesheet->new( - run => $r, mlwh_schema => $self->mlwh_schema + run => $r, + mlwh_schema => $self->mlwh_schema ); } else { $ss = npg::samplesheet::novaseq_xseries->new( - run => $r, id_run => $id_run, + id_run => $id_run, + run => $r, mlwh_schema => $self->mlwh_schema, - align => 1, keep_fastq => 1 + align => 1 ); } diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t index ca8814ca..0e28dfa1 100644 --- a/t/47-npg_samplesheet_auto.t +++ b/t/47-npg_samplesheet_auto.t @@ -93,7 +93,9 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema], is (@files, 1, 'one NovaSeqX samplesheet file is generated'); my $compare_file = 't/data/samplesheet/dragen/' . '231206_47995_NVX1_A_ssbatch98292_align.csv'; - is (slurp($files[0]), slurp($compare_file), + my $expected = slurp($compare_file); + $expected =~ s/KeepFastq,TRUE,,,/KeepFastq,FALSE,,,/; + is (slurp($files[0]), $expected, 'the NovaSeqX samplesheet is generated correctly'); } From 3caa2ab88c3b5d0160ec68f00a46817314a7c685 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 20 Dec 2023 13:11:01 +0000 Subject: [PATCH 15/28] Propagated driver details for mlwh driver --- lib/st/api/lims.pm | 41 ++++++++++++++++++++++++++++++++--------- t/40-st-lims-merge.t | 29 ++++++++++++++++++++++++++++- 2 files changed, 60 insertions(+), 10 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index e0e7a2f8..225df0ba 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -167,7 +167,6 @@ sub BUILD { my %dargs=(); my %pargs=(); my %primary_arg_type = map {$_ => 1} @{$METHODS_PER_CATEGORY{'primary'}}; - my $driver_class=$self->_driver_package_name; foreach my$k (grep {defined && $_ !~ /^_/smx} map{ $_->has_init_arg ? $_->init_arg : $_->name} @@ -198,6 +197,28 @@ sub BUILD { return; } +=head2 copy_init_args + +Returns a hash reference that can be used to initialise st::api::lims +objects similar to this object. The driver details, if present in this +object, are returned under the 'driver_type' key and, if relevant, +'mlwh_schema' key. + +=cut +sub copy_init_args { + my $self = shift; + + my %init = %{$self->_driver_arguments()}; + if ($self->driver_type()) { + $init{'driver_type'} = $self->driver_type(); + if (!$init{'mlwh_schema'} && $init{'driver_type'} =~ /warehouse/smx) { + $init{'mlwh_schema'} = $self->driver()->mlwh_schema; + } + } + + return \%init; +} + # Mapping of LIMS object types to attributes for which methods are to # be generated. These generated methods are 'plural' methods which # return an array of that attributes e.g. $lims->library_ids (returns @@ -724,7 +745,7 @@ sub _build__cached_children { my $self = shift; my @children = (); - my @basic_attrs = qw/id_run position tag_index/; + my @basic_attrs = @{$METHODS_PER_CATEGORY{'primary'}}; my $driver_type = $self->driver_type; if ($self->driver) { @@ -760,7 +781,9 @@ sub _build__cached_children { my %init = %{$self->_driver_arguments()}; $init{'driver_type'} = $driver_type; foreach my $attr (@basic_attrs) { - $init{$attr} = $component->$attr; + if ($component->can($attr)) { + $init{$attr} = $component->$attr; + } } push @children, __PACKAGE__->new(\%init); } @@ -953,7 +976,7 @@ This method can be used both as instance and as a class method. =cut -sub aggregate_libraries() { +sub aggregate_libraries { my ($self, $lane_lims_array) = @_; # This restriction might be lifted in future. @@ -975,9 +998,9 @@ sub aggregate_libraries() { # to create objects for merged entities. # Do not use $self for copying the driver arguments in order to retain # ability to use this method as a class method. - my %init = %{$lane_lims_array->[0]->_driver_arguments()}; - delete $init{position}; - delete $init{id_run}; + my $init = $lane_lims_array->[0]->copy_init_args(); + delete $init->{position}; + delete $init->{id_run}; my $merges = {}; my $lane_set_delim = q[,]; @@ -1005,7 +1028,7 @@ sub aggregate_libraries() { ->new(rpt_list => $rpt_list)->create_composition() ->freeze2rpt(); $merges->{$lane_set}->{$tag_index} = __PACKAGE__->new( - %init, rpt_list => $rpt_list + %{$init}, rpt_list => $rpt_list ); } } @@ -1045,7 +1068,7 @@ sub aggregate_libraries() { return $all_lims_objects; } -sub _check_merge_correctness{ +sub _check_merge_correctness { my $lib_lims = shift; my @lanes = uniq map {$_->position} @{$lib_lims}; if (@lanes != @{$lib_lims}) { diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index 78f8cf8c..f59aeed3 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -1,10 +1,11 @@ use strict; use warnings; -use Test::More tests => 9; +use Test::More tests => 10; use Test::Exception; use List::MoreUtils qw/all none/; use File::Slurp; use File::Temp qw/tempdir/; +use Moose::Meta::Class; use_ok('npg_tracking::glossary::rpt'); use_ok('st::api::lims'); @@ -367,6 +368,32 @@ subtest 'Multiple lane sets in aggregation by library' => sub { 'merges list - correct object, correct sort order'); }; +subtest 'mlwarehouse driver in aggregation by library' => sub { + plan tests => 5; + + my $class = Moose::Meta::Class->create_anon_class(roles=>[qw/npg_testing::db/]); + my $schema_wh = $class->new_object({})->create_test_db( + q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh] + ); + + my $id_run = 47995; + my @lane_lims = st::api::lims->new( + id_run => $id_run, + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + )->children(); + my $lims = st::api::lims->aggregate_libraries(\@lane_lims); + # Test that lims objects are viable, ie it is possible to retrieve + # their properties. + is (@{$lims->{'singles'}}, 8, 'list of singles contains 8 objects'); + lives_ok { $lims->{'singles'}->[0]->sample_name } 'can retrieve sample name'; + is (@{$lims->{'merges'}}, 87, 'list of merges contains 87 objects'); + lives_ok { $lims->{'merges'}->[0]->sample_name } 'can retrieve sample name'; + lives_ok { $lims->{'merges'}->[86]->sample_name } 'can retrieve sample name'; +}; + + sub _generate_rpt_lists { my ($id_run, $positions, $tag_indexes) = @_; my @expected_rpt_lists = (); From 68fc045dd68241d98f67444cdfccbf932cedfec1 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 2 Jan 2024 17:04:26 +0000 Subject: [PATCH 16/28] Tested objects created with the rpt_list args. The object used the ml_warehouse driver. This tests demonstrates that the children of such object are created correctly, their sample properties can be accessed. --- t/40-st-lims-mlwarehouse.t | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/t/40-st-lims-mlwarehouse.t b/t/40-st-lims-mlwarehouse.t index 483421fa..7bddaf15 100644 --- a/t/40-st-lims-mlwarehouse.t +++ b/t/40-st-lims-mlwarehouse.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 6; +use Test::More tests => 7; use Test::Exception; use_ok('st::api::lims'); @@ -164,4 +164,29 @@ subtest 'sample controls' => sub { } }; +subtest 'using rpt_list argument' => sub { + plan tests => 14; + + my $lims = st::api::lims->new( + rpt_list => '47995:1:3;47995:2:3', + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + ); + my $sample_name = '6751STDY13219555'; + is ($lims->sample_name, $sample_name, 'correct sample name'); + my @children = $lims->children(); + is (@children, 2, 'two child objects'); + for my $i ((0, 1)) { + my $child = $children[$i]; + is ($child->driver_type, 'ml_warehouse', 'child driver type is correct'); + is ($child->driver->mlwh_schema, $schema_wh, + q[child's driver is using the original db connection]); + is ($child->id_run, 47995, 'child run is is correct'); + is ($child->tag_index, 3, 'child tag index is is correct'); + is ($child->position, $i+1, 'child position is is correct'); + is ($child->sample_name, $sample_name, 'child sample name is correct'); + } +}; + 1; From c69e19f0508c37f873e1f9c2f6294d67929fa81a Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 2 Jan 2024 17:50:02 +0000 Subject: [PATCH 17/28] Fixed driver details propagation in create_lane_object method --- lib/st/api/lims.pm | 13 ++++--- t/40-st-lims-merge.t | 85 ++++++++++++++++++++++++++++++++------------ 2 files changed, 68 insertions(+), 30 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 225df0ba..8e45a63e 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -1129,13 +1129,12 @@ attributes. The new object has the same driver settings as the original object. sub create_lane_object { my ($self, $id_run, $position) = @_; ($id_run and $position) or croak 'id_run and position are expected as arguments'; - my %init = %{$self->_driver_arguments()}; - $init{'driver_type'} = $self->driver_type; - delete $init{'tag_index'}; - delete $init{'rpt_list'}; - $init{'id_run'} = $id_run; - $init{'position'} = $position; - return __PACKAGE__->new(%init); + my $init = $self->copy_init_args(); + delete $init->{'tag_index'}; + delete $init->{'rpt_list'}; + $init->{'id_run'} = $id_run; + $init->{'position'} = $position; + return __PACKAGE__->new(%{$init}); } =head2 cached_samplesheet_var_name diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index f59aeed3..d32178a8 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -12,6 +12,68 @@ use_ok('st::api::lims'); my $tmp_dir = tempdir( CLEANUP => 1 ); +my $class = Moose::Meta::Class->create_anon_class(roles=>[qw/npg_testing::db/]); +my $schema_wh = $class->new_object({})->create_test_db( + q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh] +); + +subtest 'Lane object from plex object' => sub { + plan tests => 25; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + + my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1'); + + my $e = qr/id_run and position are expected as arguments/; + throws_ok { $l->create_lane_object() } $e, 'no arguments - error'; + throws_ok { $l->create_lane_object(1) } $e, 'one argument - error'; + throws_ok { $l->create_lane_object(1, 0) } $e, + 'one of argument is false - error'; + + my $test_lane = sub { + my ($lane_l, $id_run, $position) = @_; + is ($lane_l->id_run, $id_run, "run id is $id_run"); + is ($lane_l->position, $position, "position is $position"); + is ($lane_l->rpt_list, undef, 'rpt_list is undefined'); + is ($lane_l->tag_index, undef, 'tag index is undefined'); + ok ($lane_l->is_pool, 'the entity is a pool'); + }; + + for my $p ((1,2)) { + my $lane = $l->create_lane_object(25846, $p); + $test_lane->($lane, 25846, $p); + } + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = q[]; + + my $id_run = 47995; + my @objects = (); + push @objects, st::api::lims->new( + id_run => $id_run, + position => 1, + tag_index => 1, + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + ); + + $l = st::api::lims->new( + id_run => $id_run, + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + ); + $l = ($l->children())[0]; + push @objects, ($l->children())[0]; + + for my $l_obj (@objects) { + my $lane = $l_obj->create_lane_object($id_run, 2); + is ($lane->driver->mlwh_schema, $schema_wh, + 'the original db connection is retained'); + $test_lane->($lane, $id_run, 2); + } +}; + subtest 'Aggregation across lanes for pools' => sub { plan tests => 82; @@ -133,29 +195,6 @@ subtest 'Aggregation across lanes for non-pools' => sub { _compare_properties_2($l); }; -subtest 'Aggregation across lanes for a tag' => sub { - plan tests => 13; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; - - my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1'); - - my $e = qr/id_run and position are expected as arguments/; - throws_ok { $l->create_lane_object() } $e, 'no arguments - error'; - throws_ok { $l->create_lane_object(1) } $e, 'one argument - error'; - throws_ok { $l->create_lane_object(1, 0) } $e, - 'one of argument is false - error'; - - for my $p ((1,2)) { - my $lane_l = $l->create_lane_object(25846, $p); - is ($lane_l->id_run, 25846, 'run id is 25846'); - is ($lane_l->position, $p, "position is $p"); - is ($lane_l->rpt_list, undef, 'rpt_list is undefined'); - is ($lane_l->tag_index, undef, 'tag index is undefined'); - ok ($lane_l->is_pool, 'the entity is a pool'); - } -}; - subtest 'Error conditions in aggregation by library' => sub { plan tests => 4; From 50a9edab411848c73a8b7d0123bcac05fe20f758 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 3 Jan 2024 10:57:14 +0000 Subject: [PATCH 18/28] Moved tests for creating tag zero object. Tests moved from t/40-st-lims.t to t/40-st-lims-merge.t since similar functionality for creating a lane object is tested in t/40-st-lims-merge.t t/40-st-lims.t is now left to test methods for retrieving LIMS data using the samplesheet driver. --- t/40-st-lims-merge.t | 29 +++++++++++++++++++++++++++-- t/40-st-lims.t | 22 +--------------------- 2 files changed, 28 insertions(+), 23 deletions(-) diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index d32178a8..01d4d82c 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 10; +use Test::More tests => 11; use Test::Exception; use List::MoreUtils qw/all none/; use File::Slurp; @@ -17,7 +17,7 @@ my $schema_wh = $class->new_object({})->create_test_db( q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh] ); -subtest 'Lane object from plex object' => sub { +subtest 'Create lane object from plex object' => sub { plan tests => 25; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; @@ -74,6 +74,31 @@ subtest 'Lane object from plex object' => sub { } }; +subtest 'Create tag zero object' => sub { + plan tests => 4; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + + my $l = st::api::lims->new(id_run => 25846); + throws_ok { $l->create_tag_zero_object() } qr/Position should be defined/, + 'method cannot be called on run-level object'; + $l = st::api::lims->new(rpt_list => '25846:2:1'); + throws_ok { $l->create_tag_zero_object() } qr/Position should be defined/, + 'method cannot be called on an object for a composition'; + + my $description = 'st::api::lims object, driver - samplesheet, ' . + 'id_run 25846, ' . + 'path t/data/test40_lims/samplesheet_novaseq4lanes.csv, ' . + 'position 3, tag_index 0'; + $l = st::api::lims->new(id_run => 25846, position => 3); + is ($l->create_tag_zero_object()->to_string(), $description, + 'created tag zero object from lane-level object'); + $l = st::api::lims->new(id_run => 25846, position => 3, tag_index => 5); + is ($l->create_tag_zero_object()->to_string(), $description, + 'created tag zero object from plex-level object'); +}; + subtest 'Aggregation across lanes for pools' => sub { plan tests => 82; diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 242f5662..b2c9f61d 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 16; +use Test::More tests => 15; use Test::Exception; use Test::Warn; use Moose::Meta::Class; @@ -342,26 +342,6 @@ subtest 'Samplesheet driver for arbitrary compositions' => sub { is ($ss->tag_index, 4, 'correct tag_index'); }; -subtest 'Creating tag zero object' => sub { - plan tests => 4; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; - - my $l = st::api::lims->new(id_run => 25846); - throws_ok { $l->create_tag_zero_object() } qr/Position should be defined/, - 'method cannot be called on run-level object'; - $l = st::api::lims->new(rpt_list => '25846:2:1'); - throws_ok { $l->create_tag_zero_object() } qr/Position should be defined/, - 'method cannot be called on an object for a composition'; - - my $description = 'st::api::lims object, driver - samplesheet, id_run 25846, ' . - 'path t/data/test40_lims/samplesheet_novaseq4lanes.csv, position 3, tag_index 0'; - $l = st::api::lims->new(id_run => 25846, position => 3); - is ($l->create_tag_zero_object()->to_string(), $description, 'created from lane-level object'); - $l = st::api::lims->new(id_run => 25846, position => 3, tag_index => 5); - is ($l->create_tag_zero_object()->to_string(), $description, 'created from plex-level object'); -}; - subtest 'Dual index' => sub { plan tests => 16; From 7f1213a69d23140b76e07c0bff4e68dafd010958 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 3 Jan 2024 12:02:17 +0000 Subject: [PATCH 19/28] Fixed driver details propagation in create_tag_zero_object method --- lib/st/api/lims.pm | 9 ++++----- t/40-st-lims-merge.t | 32 +++++++++++++++++++++++++++++++- 2 files changed, 35 insertions(+), 6 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 8e45a63e..08713f95 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -1092,7 +1092,7 @@ sub _check_value_is_unique { =head2 create_tag_zero_object -Using id_run and position values of this object, creates and returns +Using run ID and position values of this object, creates and returns st::api::lims object for tag zero. The new object has the same driver settings as the original object. @@ -1109,10 +1109,9 @@ sub create_tag_zero_object { if (!defined $self->position) { croak 'Position should be defined'; } - my %init = %{$self->_driver_arguments()}; - $init{'driver_type'} = $self->driver_type; - $init{'tag_index'} = 0; - return __PACKAGE__->new(%init); + my $init = $self->copy_init_args(); + $init->{'tag_index'} = 0; + return __PACKAGE__->new(%{$init}); } =head2 create_lane_object diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index 01d4d82c..d4d7a125 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -75,7 +75,7 @@ subtest 'Create lane object from plex object' => sub { }; subtest 'Create tag zero object' => sub { - plan tests => 4; + plan tests => 10; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; @@ -97,6 +97,36 @@ subtest 'Create tag zero object' => sub { $l = st::api::lims->new(id_run => 25846, position => 3, tag_index => 5); is ($l->create_tag_zero_object()->to_string(), $description, 'created tag zero object from plex-level object'); + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = q[]; + + my $id_run = 47995; + my @objects = (); + push @objects, st::api::lims->new( + id_run => $id_run, + position => 1, + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + ); + + $l = st::api::lims->new( + id_run => $id_run, + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + ); + $l = ($l->children())[0]; + push @objects, ($l->children())[0]; + + for my $l_obj (@objects) { + my $t0 = $l_obj->create_tag_zero_object(); + is ($t0->driver->mlwh_schema, $schema_wh, + 'the original db connection is retained'); + my @names = $t0->sample_names(); + is (@names, 18, '18 sample names are retrieved'); + is ($names[0], '6751STDY13219539', 'first sample name is correct'); + } }; subtest 'Aggregation across lanes for pools' => sub { From de55a4b5d2ba1daef166d0acafb1702429ffdfee Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 3 Jan 2024 12:29:30 +0000 Subject: [PATCH 20/28] Updated aggregate_xlanes method ... to use copy_init_args method instead of _driver_arguments method mostly in order to be consistent. Since this method is called in the run-level object, it does not suffer from the same problems as other methods, which had to be updated in this pr. All new tests for this commit passed without changing the code. --- lib/st/api/lims.pm | 11 +++++------ t/40-st-lims-merge.t | 34 ++++++++++++++++++++++++++++++++-- 2 files changed, 37 insertions(+), 8 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 08713f95..e8367094 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -897,9 +897,8 @@ sub aggregate_xlanes { return; }; # End of test function - my %init = %{$self->_driver_arguments()}; - $init{'driver_type'} = $self->driver_type; - delete $init{'id_run'}; + my $init = $self->copy_init_args(); + delete $init->{'id_run'}; my $lims4compisitions = {}; my @test_attrs = qw/sample_id library_id/; @@ -908,7 +907,7 @@ sub aggregate_xlanes { if (!@pools) { $can_merge->(\@lanes, @test_attrs); # Test consistency - push @aggregated, __PACKAGE__->new(%init, rpt_list => $lanes_rpt_list); + push @aggregated, __PACKAGE__->new(%{$init}, rpt_list => $lanes_rpt_list); } else { my @sizes = uniq (map { $_->num_children } @lanes); if (@sizes != 1) { # Test consistency @@ -925,11 +924,11 @@ sub aggregate_xlanes { my $ea = each_arrayref map { [$_->children()] } @lanes; while ( my @plexes = $ea->() ) { $can_merge->(\@plexes, @test_attrs, 'tag_index'); # Test consistency - push @aggregated, __PACKAGE__->new(%init, + push @aggregated, __PACKAGE__->new(%{$init}, rpt_list => npg_tracking::glossary::rpt->deflate_rpts(\@plexes)); } # Add object for tag zero - push @aggregated, __PACKAGE__->new(%init, + push @aggregated, __PACKAGE__->new(%{$init}, rpt_list => npg_tracking::glossary::rpt->tag_zero_rpt_list($lanes_rpt_list)); } diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index d4d7a125..4fd4aa7c 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -130,9 +130,10 @@ subtest 'Create tag zero object' => sub { }; subtest 'Aggregation across lanes for pools' => sub { - plan tests => 82; + plan tests => 89; - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; my $l = st::api::lims->new(rpt_list => '25846:1:3'); throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, @@ -235,6 +236,35 @@ subtest 'Aggregation across lanes for pools' => sub { 'sample names including spiked phix'); is (join(q[:], $tag_zero->sample_names(1)), join(q[:], @sample_names), 'sample names including spiked phix'); + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = q[]; + + my $id_run = 47995; + $l = st::api::lims->new( + id_run => $id_run, + id_flowcell_lims => 98292, + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + ); + + @merged = $l->aggregate_xlanes(qw/1 2/); + is (scalar @merged, 19, 'number of aggregates is number of tags plus two'); + $tag_zero = pop @merged; + $tag_spiked = pop @merged; + $tag_last = pop @merged; + $tag_first = shift @merged; + is ($tag_zero->rpt_list, "$id_run:1:0;$id_run:2:0", + 'rpt list for tag zero object'); + my @tag_zero_sample_names = $tag_zero->sample_names(); + is (@tag_zero_sample_names, 18, '18 sample names are retrieved'); + is ($tag_zero_sample_names[0], '6751STDY13219539', + 'first sample name is correct'); + is ($tag_spiked->rpt_list, "$id_run:1:888;$id_run:2:888", + 'rpt list for spiked in tag object'); + is ($tag_last->rpt_list, "$id_run:1:17;$id_run:2:17", + 'rpt list for tag 21 object'); + is ($tag_first->rpt_list, "$id_run:1:1;$id_run:2:1", + 'rpt list for tag 1 object'); }; subtest 'Aggregation across lanes for non-pools' => sub { From a2011043a32b1c97e86e95a32a3beec49a7b2ee6 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 4 Jan 2024 10:59:05 +0000 Subject: [PATCH 21/28] Removed st::api::lims batch_id constructor arg. Was needed when we used the xml driver. No current lims driver is using this argument. Existing production code does not pass batch_id to st::api::lims constructor. st::api::lims documentation updated. --- lib/st/api/lims.pm | 52 +++++++++++++++++++++++++++++++--------------- t/40-st-lims.t | 4 ++-- 2 files changed, 37 insertions(+), 19 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index e0e7a2f8..21563a21 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -21,27 +21,46 @@ st::api::lims =head1 SYNOPSIS - $lims = st::api::lims->new(id_run => 333); #run (batch) level object - $lims = st::api::lims->new(batch_id => 222); # as above - $lims = st::api::lims->new(batch_id => 222, position => 3); # lane level object - $lims = st::api::lims->new(id_run => 333, position => 3, tag_index => 44); # plex level object - $lims = st::api::lims->new(rpt_list => '333:3:44'); # object for a one-component composition - $lims = st::api::lims->new(rpt_list => '333:3:44;333:4:44;'); # object for a two-component composition - $lims = st::api::lims->new(driver_type => q(ml_warehouse), flowcell_barcode => q(HTC3HADXX), - position => 2, tag_index => 40); # plex level object from ml_warehouse - $lims = st::api::lims->new(driver_type => q(ml_warehouse), flowcell_barcode => q(HTC3HADXX), - position => 2, tag_index => 40, mlwh_schema=>$suitable_dbic_schema); + # Run level object + $lims = st::api::lims->new(id_run => 333); + $lims = st::api::lims->new(driver_type => q(ml_warehouse), + flowcell_barcode => q(HTC3HADXX)); + + # Lane level object + $lims = st::api::lims->new(id_run => 333, position => 3); + + # Plex level object + $lims = st::api::lims->new(id_run => 333, position => 3, tag_index => 44); + $lims = st::api::lims->new(driver_type => q(ml_warehouse), + id_flowcell_lims => 222, + position => 2, + tag_index => 40, + mlwh_schema=>$suitable_dbic_schema); + + # Objects defined via a list of one or more rpt values + $lims = st::api::lims->new(rpt_list => '333:3:44'); + $lims = st::api::lims->new(rpt_list => '333:3:44;333:4:44;'); =head1 DESCRIPTION -Generic NPG pipeline oriented LIMS wrapper capable of retrieving data from multiple sources -(drivers). Provides methods performing "business" logic independent of data source. +Generic NPG LIMS wrapper capable of retrieving data from multiple sources via +a number of source-specific drivers. Provides methods implementing business +logic that is independent of data source. -Note the set of valid arguments to the constructor are a function of the driver_type passed. +A set of valid arguments to the constructor depends on the driver type. The +drivers are implemented as st::api::lims:: classes. -Any driver attribute can be passed through to the driver's constructor via this objects's -constructor. Not all of the attributes passed through to the driver will be available -as this object's accessors. Example: +The default driver type is 'samplesheet'. The path to the samplesheet can be +set either in the 'path' constructor attribute or by setting the env. variable +NPG_CACHED_SAMPLESHEET_FILE. + +All flavours of the ml_warehouse driver require access to the ml warehouse +database. If the mlwh_schema constructor argument is not set, a connection +to the database defined in a standard NPG configuration file is be used. + +Any driver attribute can be passed through to the driver's constructor via +this objects's constructor. Not all of the attributes passed through to the +driver are be available as this object's attributes. Example: $lims = st::api::lims->new( id_flowcell_lims => 34567, @@ -72,7 +91,6 @@ Readonly::Hash my %METHODS_PER_CATEGORY => { id_run path id_flowcell_lims - batch_id flowcell_barcode rpt_list /], diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 242f5662..2210b4be 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -89,9 +89,9 @@ subtest 'Driver type, methods and driver build' => sub { }; subtest 'Setting return value for primary attributes' => sub { - plan tests => 23; + plan tests => 21; - my @other = qw/batch_id id_flowcell_lims flowcell_barcode/; + my @other = qw/id_flowcell_lims flowcell_barcode/; my $ss_path = 't/data/samplesheet/miseq_default.csv'; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $ss_path; From 770e6a1d014505022c3ef15b98ab0695a6d98921 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 4 Jan 2024 14:20:28 +0000 Subject: [PATCH 22/28] Better phrasing --- lib/st/api/lims.pm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 21563a21..fe32b736 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -59,8 +59,8 @@ database. If the mlwh_schema constructor argument is not set, a connection to the database defined in a standard NPG configuration file is be used. Any driver attribute can be passed through to the driver's constructor via -this objects's constructor. Not all of the attributes passed through to the -driver are be available as this object's attributes. Example: +the constructor of the st::api::lims object. Not all of the attributes passed +through to the driver are be available as this object's attributes. Example: $lims = st::api::lims->new( id_flowcell_lims => 34567, From 9a2c9f0a29aeab37388b0716af7d057aaedea986 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 4 Jan 2024 16:14:19 +0000 Subject: [PATCH 23/28] Ability to derive id_run from a run record The old samplesheet generator had this ability. Rearranged the code so that the samplesheet generator for NovaSeqX also has this ability, which simplifies the code in the samplesheet daemon. NovaSeqX samplesheet generator retains ability to generate a samplesheet when neither id_run nor the run db record is set via the constructor. --- lib/npg/samplesheet.pm | 20 +------------------- lib/npg/samplesheet/auto.pm | 5 +++-- lib/npg/samplesheet/base.pm | 10 +++++++++- lib/npg/samplesheet/novaseq_xseries.pm | 26 +++++++++++++++++++++++--- t/47-npg_samplesheet_novaseq_xseries.t | 16 +++++++++++++--- 5 files changed, 49 insertions(+), 28 deletions(-) diff --git a/lib/npg/samplesheet.pm b/lib/npg/samplesheet.pm index ea70c816..72486c38 100755 --- a/lib/npg/samplesheet.pm +++ b/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 Edavid.jackson@sanger.ac.ukE =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. diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index f014b9ea..f397506e 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -155,7 +155,6 @@ sub process { ); } else { $ss = npg::samplesheet::novaseq_xseries->new( - id_run => $id_run, run => $r, mlwh_schema => $self->mlwh_schema, align => 1 @@ -307,6 +306,8 @@ __END__ =item Carp +=item List::MoreUtils + =item npg_tracking::Schema =item npg::samplesheet @@ -327,7 +328,7 @@ David K. Jackson Edavid.jackson@sanger.ac.ukE =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. diff --git a/lib/npg/samplesheet/base.pm b/lib/npg/samplesheet/base.pm index 866918c7..d8e7d05c 100755 --- a/lib/npg/samplesheet/base.pm +++ b/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 Emg8@sanger.ac.ukE =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. diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index 18694210..32551333 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -10,7 +10,9 @@ 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'; @@ -100,7 +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'; } @@ -137,7 +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; @@ -187,10 +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 ' . @@ -867,6 +883,10 @@ __END__ =item Data::UUID +=item Try::Tiny + +=item npg_tracking::util::types + =back =head1 BUGS AND LIMITATIONS @@ -879,7 +899,7 @@ Marina Gourtovaia Emg8@sanger.ac.ukE =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 diff --git a/t/47-npg_samplesheet_novaseq_xseries.t b/t/47-npg_samplesheet_novaseq_xseries.t index 9778f372..9dad14c3 100644 --- a/t/47-npg_samplesheet_novaseq_xseries.t +++ b/t/47-npg_samplesheet_novaseq_xseries.t @@ -26,7 +26,7 @@ my $schema_wh = $class->new_object({})->create_test_db( my $date = DateTime->now()->strftime('%y%m%d'); subtest 'create the generator object, test simple attributes' => sub { - plan tests => 17; + plan tests => 19; my $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, @@ -107,11 +107,21 @@ subtest 'create the generator object, test simple attributes' => sub { id_run => 47446, samplesheet_path => "$dir/one/" ); + my $expected_file_name = "${date}_47446_NVX1_B_ssbatch99888.csv"; my $file_name = $g->file_name; - is ($file_name, "${date}_47446_NVX1_B_ssbatch99888.csv", - 'correct file name is generated'); + is ($file_name, $expected_file_name, 'correct file name is generated'); is ($g->output, "$dir/one/$file_name", 'correct output path is generated'); + $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + run => $run_row, + samplesheet_path => "$dir/one/" + ); + $file_name = $g->file_name; + is ($file_name, $expected_file_name, 'correct file name is generated'); + is ($g->output, "$dir/one/$file_name", 'correct output path is generated'); + $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, From cc116b6a8c1fd05c1126eb03aa50b271675e3e4e Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 9 Jan 2024 18:22:07 +0000 Subject: [PATCH 24/28] Recorded recent changes --- Changes | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/Changes b/Changes index 0c7789aa..7ad9e0d3 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,20 @@ 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. + release 98.1.0 - Added a new method, latest_revision_for_modification, to npg_tracking::Schema::Result::Instrument to retrieve the latest modification From 71bc5ae8d57b346c28d6ea7cf700617148388d65 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 17 Jan 2024 16:30:17 +0000 Subject: [PATCH 25/28] update signature and iRODS documentation link --- Changes | 1 + .../templates/run_status2followers.tt2 | 2 +- data/npg_tracking_email/templates/wrapper.tt2 | 2 +- t/80-npg_tracking-report-event2subscribers.t | 14 +++++++------- t/data/report/report_text_1 | 2 +- t/data/report/report_text_5 | 4 ++-- 6 files changed, 13 insertions(+), 12 deletions(-) diff --git a/Changes b/Changes index 7ad9e0d3..ec59ecb1 100644 --- a/Changes +++ b/Changes @@ -14,6 +14,7 @@ LIST OF CHANGES - 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 release 98.1.0 - Added a new method, latest_revision_for_modification, to diff --git a/data/npg_tracking_email/templates/run_status2followers.tt2 b/data/npg_tracking_email/templates/run_status2followers.tt2 index 8289a6f1..38c6fd5a 100644 --- a/data/npg_tracking_email/templates/run_status2followers.tt2 +++ b/data/npg_tracking_email/templates/run_status2followers.tt2 @@ -11,7 +11,7 @@ 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: diff --git a/data/npg_tracking_email/templates/wrapper.tt2 b/data/npg_tracking_email/templates/wrapper.tt2 index ddc9998b..a125e281 100644 --- a/data/npg_tracking_email/templates/wrapper.tt2 +++ b/data/npg_tracking_email/templates/wrapper.tt2 @@ -1,2 +1,2 @@ [% content %] -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP diff --git a/t/80-npg_tracking-report-event2subscribers.t b/t/80-npg_tracking-report-event2subscribers.t index 0aeb8372..2d7347c2 100644 --- a/t/80-npg_tracking-report-event2subscribers.t +++ b/t/80-npg_tracking-report-event2subscribers.t @@ -156,7 +156,7 @@ Run 21915 was assigned status "run pending" on 2017-02-08 11:49:39 by joe_events NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT is ($e->report_full(), $report, 'full report text'); @@ -173,7 +173,7 @@ $lims_summary NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT1 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); @@ -217,7 +217,7 @@ Instrument HS8 status changed to "wash performed" on $date_as_string by joe_appr NPG page for this instrument: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT2 is ($e->report_full($e->lims()), $report, 'full report text'); @@ -231,7 +231,7 @@ Instrument HS8 status changed to "wash performed" on $date_as_string by joe_appr NPG page for this instrument: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT3 is ($e->report_full($e->lims()), $report, 'full report text with a comment'); is (scalar @{$e->reports}, 1, 'One report generated'); @@ -272,7 +272,7 @@ $lims_summary NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT4 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); }; @@ -325,7 +325,7 @@ Lane 2: Samples NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT5 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); }; @@ -362,7 +362,7 @@ Instrument HS8 annotated by joe_loader on $date_as_string - New instrument annot NPG page for this instrument: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT6 is ($e->report_full($e->lims()), $report, 'full report text'); }; diff --git a/t/data/report/report_text_1 b/t/data/report/report_text_1 index cc591d00..58a0bf08 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -37,5 +37,5 @@ Analysis and QC information for this run will be/is available: http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915 http://sfweb.internal.sanger.ac.uk:1959/checks/runs/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP diff --git a/t/data/report/report_text_5 b/t/data/report/report_text_5 index 46ad211f..ef72e655 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -36,7 +36,7 @@ Lane 7: Samples ... 6 samples in total -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 ). NPG page for the run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 @@ -45,5 +45,5 @@ Analysis and QC information for this run will be/is available: http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915 http://sfweb.internal.sanger.ac.uk:1959/checks/runs/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP From ae982c23621da58234053373811d044e64d5c92b Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 18 Jan 2024 14:27:14 +0000 Subject: [PATCH 26/28] use https for tracking urls in emails --- Changes | 1 + data/npg_tracking_email/templates/urls.tt2 | 2 +- t/80-npg_tracking-report-event2subscribers.t | 14 +++++++------- t/data/report/report_text_1 | 2 +- t/data/report/report_text_5 | 2 +- 5 files changed, 11 insertions(+), 10 deletions(-) diff --git a/Changes b/Changes index ec59ecb1..bbd4f89b 100644 --- a/Changes +++ b/Changes @@ -15,6 +15,7 @@ LIST OF CHANGES 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 release 98.1.0 - Added a new method, latest_revision_for_modification, to diff --git a/data/npg_tracking_email/templates/urls.tt2 b/data/npg_tracking_email/templates/urls.tt2 index dcca50be..c0e48511 100644 --- a/data/npg_tracking_email/templates/urls.tt2 +++ b/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'; %] \ No newline at end of file diff --git a/t/80-npg_tracking-report-event2subscribers.t b/t/80-npg_tracking-report-event2subscribers.t index 2d7347c2..39264a9f 100644 --- a/t/80-npg_tracking-report-event2subscribers.t +++ b/t/80-npg_tracking-report-event2subscribers.t @@ -154,7 +154,7 @@ Run 21915 was assigned status "run pending" on 2017-02-08 11:49:39 by joe_events NPG page for this run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 NPG on behalf of DNA Pipelines and GSLP REPORT @@ -171,7 +171,7 @@ Run 21915 was assigned status "run pending" on 2017-02-08 11:49:39 by joe_events $lims_summary NPG page for this run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 NPG on behalf of DNA Pipelines and GSLP REPORT1 @@ -215,7 +215,7 @@ subtest 'instrument status event' => sub { Instrument HS8 status changed to "wash performed" on $date_as_string by joe_approver NPG page for this instrument: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/instrument/HS8 NPG on behalf of DNA Pipelines and GSLP REPORT2 @@ -229,7 +229,7 @@ REPORT2 Instrument HS8 status changed to "wash performed" on $date_as_string by joe_approver. Comment: my comment NPG page for this instrument: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/instrument/HS8 NPG on behalf of DNA Pipelines and GSLP REPORT3 @@ -270,7 +270,7 @@ Run 21915 annotated by joe_loader on $date_as_string - New run annotation $lims_summary NPG page for this run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 NPG on behalf of DNA Pipelines and GSLP REPORT4 @@ -323,7 +323,7 @@ Lane 2: Samples NPG page for this run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 NPG on behalf of DNA Pipelines and GSLP REPORT5 @@ -360,7 +360,7 @@ subtest 'instrument annotation event' => sub { Instrument HS8 annotated by joe_loader on $date_as_string - New instrument annotation NPG page for this instrument: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/instrument/HS8 NPG on behalf of DNA Pipelines and GSLP REPORT6 diff --git a/t/data/report/report_text_1 b/t/data/report/report_text_1 index 58a0bf08..25c4b581 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -31,7 +31,7 @@ Lane 3: Samples Sequencing and default analysis for this run completed. Run is now pending manual QC review. Meanwhile, we will be loading analysis results into iRODS. NPG page for the run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 Analysis and QC information for this run will be/is available: http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915 diff --git a/t/data/report/report_text_5 b/t/data/report/report_text_5 index ef72e655..667b55b3 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -39,7 +39,7 @@ Lane 7: Samples 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 ). NPG page for the run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 Analysis and QC information for this run will be/is available: http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915 From 8b955db08e5e1ab7d84715b4cadfa0fccc522d03 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 17 Jan 2024 17:01:10 +0000 Subject: [PATCH 27/28] remove illumina lane qc link from emails --- Changes | 2 ++ data/npg_tracking_email/templates/run_status2followers.tt2 | 1 - t/data/report/report_text_1 | 1 - t/data/report/report_text_5 | 1 - 4 files changed, 2 insertions(+), 3 deletions(-) diff --git a/Changes b/Changes index bbd4f89b..43e91f1a 100644 --- a/Changes +++ b/Changes @@ -16,6 +16,8 @@ LIST OF CHANGES - 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 diff --git a/data/npg_tracking_email/templates/run_status2followers.tt2 b/data/npg_tracking_email/templates/run_status2followers.tt2 index 38c6fd5a..d77bb51d 100644 --- a/data/npg_tracking_email/templates/run_status2followers.tt2 +++ b/data/npg_tracking_email/templates/run_status2followers.tt2 @@ -18,6 +18,5 @@ 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 %] diff --git a/t/data/report/report_text_1 b/t/data/report/report_text_1 index 25c4b581..b19b4651 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -34,7 +34,6 @@ NPG page for the run: https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 Analysis and QC information for this run will be/is available: -http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915 http://sfweb.internal.sanger.ac.uk:1959/checks/runs/21915 NPG on behalf of DNA Pipelines and GSLP diff --git a/t/data/report/report_text_5 b/t/data/report/report_text_5 index 667b55b3..ca961e6d 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -42,7 +42,6 @@ NPG page for the run: https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 Analysis and QC information for this run will be/is available: -http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915 http://sfweb.internal.sanger.ac.uk:1959/checks/runs/21915 NPG on behalf of DNA Pipelines and GSLP From 1f2984a4f2dfaa97c1aca94dc4170540b2251486 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Tue, 23 Jan 2024 13:41:02 +0000 Subject: [PATCH 28/28] prep release 99.0.0 --- Changes | 1 + 1 file changed, 1 insertion(+) diff --git a/Changes b/Changes index 43e91f1a..d4d3048b 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,6 @@ 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.