diff --git a/Build.PL b/Build.PL index 942085ca..f9da0065 100644 --- a/Build.PL +++ b/Build.PL @@ -140,6 +140,7 @@ my $builder = $class->new( 'DBIx::Class' => '0.08119', 'DBIx::Class::Core' => 0, 'DBIx::Class::Schema' => 0, + 'DBIx::Class::Schema::Loader' => 0, 'DBIx::Class::InflateColumn::DateTime' => 0, 'Digest::MD5' => 0, 'Digest::SHA' => 0, diff --git a/Changes b/Changes index a46e2ca0..319702e2 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,17 @@ LIST OF CHANGES +release 96.0.0 + - Fixed a regression in the npg_move_runfolder script, + which made it unusable. + - Rejig run folder tracking function into method + - Stop using XML LIMS data in a test + - Import samplesheet daemon + - Ensure we have a loader to generate ORM classes + - Flagged planned onboard analysis + - locate_runfolder: simplify, cope with complex globs, link page for multiple + locations + - Allow NovaSeqX samplesheets to embed instrument and slot + release 95.0.0 - Remove singularity recipe and related files - Import mlwh drivers diff --git a/MANIFEST b/MANIFEST index 75dd884c..e67a01cf 100644 --- a/MANIFEST +++ b/MANIFEST @@ -3,6 +3,7 @@ bin/event_notifications bin/illumina_instruments_uptime bin/npg_daemon_control bin/npg_move_runfolder +bin/npg_samplesheet4MiSeq bin/npg_status_save bin/staging_area_monitor bin/npg_deletable_dr_runs @@ -164,6 +165,7 @@ lib/npg_tracking/report/event2subscribers.pm lib/npg_tracking/report/events.pm lib/npg/samplesheet.pm lib/npg/samplesheet/novaseq_xseries.pm +lib/npg/samplesheet/auto.pm lib/npg/util.pm lib/npg/util/mailer.pm lib/npg/view.pm @@ -404,6 +406,7 @@ t/30-api-util.t t/34-monitor-runfolder-staging.t t/34-monitor-runfolder.t t/34-monitor-staging.t +t/35-monitor_one_runfolder.t t/40-st-base.t t/40-st-batch.t t/40-st-lims-insert_size.t @@ -417,6 +420,7 @@ t/40-st-study.t t/45-st-api-lims-traversal.t t/47-samplesheet.t t/47-npg_samplesheet_novaseq_xseries.t +t/47-npg_samplesheet_auto.t t/50-controller.t t/50-decorator.t t/60-illumina-runfolder.t @@ -481,6 +485,9 @@ t/data/fixtures/400-run_status.yml t/data/fixtures/400-tag_run.yml t/data/fixtures/400-tag_run_lane.yml t/data/fixtures/500-st_cache.yml +t/data/fixtures_lims_transcriptome/000-Sample.yml +t/data/fixtures_lims_transcriptome/000-Study.yml +t/data/fixtures_lims_transcriptome/100-IseqFlowcell.yml t/data/fixtures_lims_wh/00-IseqRunStatusDict.yml t/data/fixtures_lims_wh/000-Sample.yml t/data/fixtures_lims_wh/000-Study.yml @@ -723,6 +730,7 @@ t/data/run_params/RunParameters.novaseq.xml t/data/run_params/RunParameters.novaseq.xp.xml t/data/run_params/RunParameters.novaseq.xp.v1.5.xml t/data/run_params/RunParameters.novaseqx.xml +t/data/run_params/RunParameters.novaseqx.onboard.xml t/data/run_params/runParameters.hiseq.rr.single.xml t/data/run_params/runParameters.hiseq.rr.twoind.xml t/data/run_params/runParameters.hiseq.rr.xml @@ -1339,6 +1347,8 @@ t/data/test45/st/studies/297.xml t/data/test45/st/studies/333.xml t/data/test45/st/studies/365.xml t/data/test45/st/studies/700.xml +t/data/test_staging_daemon/novaseqxplus/RunInfo.xml +t/data/test_staging_daemon/novaseqxplus/RunParameters.xml t/data/gaii/staging/IL12/incoming/100721_IL12_05222/Data/Intensities/L001/.gitignore t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore diff --git a/bin/npg_move_runfolder b/bin/npg_move_runfolder index 8314ea73..f43d5d69 100755 --- a/bin/npg_move_runfolder +++ b/bin/npg_move_runfolder @@ -1,26 +1,36 @@ #!/usr/bin/env perl -######### -# Author: js10 -# Created: 2018-05-30 -# use strict; use warnings; - use FindBin qw($Bin); use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" ); -use Carp; -use autodie qw(:all); +use Getopt::Long; +use Pod::Usage; -use Monitor::Staging; use Monitor::RunFolder::Staging; our $VERSION = '0'; -use Readonly; +my $help; +my $runfolder_path; +my $status_update = 0; + +GetOptions ( + 'help' => \$help, + 'runfolder_path=s' => \$runfolder_path, + 'status_update!' => \$status_update, +); +if ($help) { pod2usage(0); } + +if (!defined $runfolder_path || $runfolder_path == q[]) { + die "ERROR: --runfolder_path argument is required\n"; +} + +my @ms = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + status_update => $status_update +)->move_to_analysis(); -my $mon = Monitor::RunFolder::Staging->new_with_options(status_update => 0); -my @ms = $mon->move_to_analysis(); print join "\n", @ms; 1; @@ -30,23 +40,38 @@ __END__ =head1 NAME -npg_move_runfolder - move 'incoming' to 'analysis' and change group. +npg_move_runfolder - move the run folder given as an argument from +'incoming' to 'analysis' and change group. =head1 VERSION =head1 SYNOPSIS - C + C =head1 DESCRIPTION -This script moves a given run folder from 'incoming' directory to 'analysis' directory -and changes the group name to that found in the staging configuration. -By default it does not change the run status. +This script moves a given run folder from 'incoming' directory to 'analysis' +directory and changes the group name to that found in the staging +configuration. By default it does not change the run status. + +=head1 REQUIRED ARGUMENTS + + C + +=head1 OPTIONS + + C - displays help message and exists + + C - the path of the run folder, required + + C - a boolean option, defaults to false, meaning that + the run status update is not performed =head1 CONFIGURATION AND ENVIRONMENT -Depends on the presence of the npg tracking system. +If the run status update is performed, write access to the tracking +database is required. =head1 INCOMPATIBILITIES @@ -58,7 +83,7 @@ Jennifer Liddle, Ejs10@sanger.ac.ukE =head1 LICENCE AND COPYRIGHT -Copyright (C) 2018 GRL, by Jennifer Liddle +Copyright (C) 2018, 2023 Genome Research Ltd. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by diff --git a/bin/npg_samplesheet4MiSeq b/bin/npg_samplesheet4MiSeq new file mode 100755 index 00000000..c97cc99f --- /dev/null +++ b/bin/npg_samplesheet4MiSeq @@ -0,0 +1,96 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use FindBin qw($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'); + +npg::samplesheet::auto->new()->loop(); + +0; + +__END__ + +=head1 NAME + +npg_samplesheet4MiSeq + +=head1 USAGE + + npg_samplesheet4MiSeq + +=head1 DESCRIPTION + +The script, once started, runs in perpetuity, generating Illumina-style +samplesheets for any MiSeq run with status 'run pending'. + +=head1 REQUIRED ARGUMENTS + +None + +=head1 OPTIONS + +=head1 DIAGNOSTICS + +=head1 CONFIGURATION + +=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 + +Jaime Tovar Ejmtc@sanger.ac.ukE + +=head1 LICENSE AND COPYRIGHT + +Copyright (C) 2020,2021,2023 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/staging_area_monitor b/bin/staging_area_monitor index 71cfca26..1ed21c40 100755 --- a/bin/staging_area_monitor +++ b/bin/staging_area_monitor @@ -19,9 +19,6 @@ our $VERSION = '0'; Readonly::Scalar my $SLEEP_INTERVAL => 60 * 15; Readonly::Scalar my $DRY_RUN => $ENV{'dev'} && ($ENV{'dev'} ne 'live'); -Readonly::Array my @UPDATES_FOR_INCOMING_ALLOWED_STATUSES => - ('run pending', 'run in progress', 'run complete'); -Readonly::Scalar my $USERNAME => 'pipeline'; local $OUTPUT_AUTOFLUSH = 1; @@ -39,147 +36,6 @@ _log_noindent($DRY_RUN ? 'DRY RUN, no run folder moves' : 'LIVE RUN'); main(); -sub check_path { ##### Function to deal with one run folder - my ($run_path, $schema, $previous_size_of) = @_; - - my $folder = Monitor::RunFolder::Staging->new( - runfolder_path => $run_path, - npg_tracking_schema => $schema); - $run_path = $folder->runfolder_path; # in case path was transformed - - my $run_status = $folder->tracking_run()->current_run_status_description(); - my $id_run = $folder->tracking_run()->id_run; - - _log("Run $id_run status $run_status"); - if ($folder->platform_NovaSeqX()) { - _log("... run on NovaSeqX instrument"); - } - - my $db_flowcell_barcode = $folder->tracking_run()->flowcell_id; - my $staging_flowcell_barcode = $folder->run_flowcell; # from RunParameters.xml - $staging_flowcell_barcode ||= q[]; - if ($db_flowcell_barcode) { # database flowcell barcode validation - if ($db_flowcell_barcode ne $staging_flowcell_barcode) { - croak 'Flowcell barcode mismatch between database and staging: ' . - join q[ ], $db_flowcell_barcode, $staging_flowcell_barcode; - } - } else { # save flowcell barcode to the tracking database - $staging_flowcell_barcode or croak - "Staging flowcell barcode is not defined for run $id_run"; - _log("Saving staging flowcell barcode $staging_flowcell_barcode to the database."); - $folder->tracking_run()->update({flowcell_id => $staging_flowcell_barcode}); - } - - if ($folder->is_in_analysis) { - _log('Folder is in /analysis/'); - - if( $run_status eq 'qc complete') { - _log('Moving run folder to /outgoing/'); - (not $DRY_RUN) and _log($folder->move_to_outgoing()); - } - return; # Nothing else to do for a folder in /analysis/ - } - - _log('Folder is in /incoming/'); - - # If we don't remember seeing it before, set the folder name and glob; - # set staging tag, if appropriate, set/fix instrument side, workflow side. - # Previously we avoided making changes to the db if status was at or after - # 'run complete'. We might consider reinstating this rule. - if ( not defined $previous_size_of->{$run_path} ) { - $folder->update_run_record(); - $folder->tracking_run()->set_tag( $USERNAME, 'staging' ); - _log('Set staging tag'); - try { - my $iside = $folder->set_instrument_side(); - if ($iside) { - _log("Instrument side is set to $iside"); - } - my $wf_type = $folder->set_workflow_type(); - if ($wf_type) { - _log("Workflow type is set to $wf_type"); - } - $folder->set_run_tags(); - } catch { - _log('Error: ' . $_); - }; - - $previous_size_of->{$run_path} = 0; - } - - # Could delete the directory here. Leave it for now. - return if $run_status eq 'data discarded'; - - if (any { $run_status eq $_ } @UPDATES_FOR_INCOMING_ALLOWED_STATUSES) { - - my $latest_cycle = $folder->get_latest_cycle(); - if ($folder->update_cycle_count($latest_cycle)) { - _log("Cycle count updated to $latest_cycle"); - } - - if ( $run_status eq 'run pending' ) { - - if ($latest_cycle) { - $folder->update_run_status('run in progress'); - _log(q[Run status updated to 'run in progress']); - } - - } elsif ( $run_status eq 'run in progress' ) { - - # The lane count comes from the run folder structure, which - # we should have by now set up. - $folder->delete_superfluous_lanes(); - if ($folder->is_run_complete()) { - $folder->update_run_status('run complete'); - _log(q[Run status updated to 'run complete']); - } - - } else { # run status is 'run complete' - - $folder->update_run_record(); # Inspect and update cycles, - # including expected cycle count! - - if ( $folder->check_tiles($run_path) ) { - - my $previous_size = $previous_size_of->{$run_path}; - my ( $current_size, $latest_mod ) = $folder->monitor_stats(); - _log(sprintf 'Run folder sizes: previous %i, current %i', - $previous_size, $current_size); - $previous_size_of->{$run_path} = $current_size; - - if ( $current_size != $previous_size ) { - _log('Runfolder size is still changing.'); - return; - } - - # Check that no file is 'in the future'. - if ( $latest_mod > time ) { - _log("Files in 'future' $latest_mod are present."); - return; - } - - # Check if we are waiting for the onboard analysis to finish. - if ($folder->is_onboard_analysis_planned() && - !$folder->is_onboard_analysis_output_copied()) { - return; - } - - # Set status to 'run mirrored' and move run folder - # from /incoming/ to /analysis/ - $folder->update_run_status('run mirrored'); - _log(q[Run status updated to 'run mirrored']); - _log('Moving run folder to analysis'); - (not $DRY_RUN) and _log($folder->move_to_analysis()); - - return 'done'; - } - } - } - - return; - -} ###### End of function to deal with one run folder - ########################################################### ############### Main daemon loop. ###################### ########################################################### @@ -204,7 +60,9 @@ sub main { _log_noindent("Considering $run_path"); my $done; try { - $done = check_path($run_path, $schema, $previous_size_of); + $done = Monitor::RunFolder::Staging->new( + runfolder_path => $run_path, + npg_tracking_schema => $schema)->update_run_from_path($previous_size_of, $DRY_RUN); } finally { if (@_) { _log("ERROR: Execution for $run_path died with: @_\n"); diff --git a/cgi-bin/locate_runfolder b/cgi-bin/locate_runfolder index f020510c..f9de38c0 100755 --- a/cgi-bin/locate_runfolder +++ b/cgi-bin/locate_runfolder @@ -25,6 +25,19 @@ sub _error { return; } +sub _list_folders { + my @list = @_; + print "Content-type: text/html\n\n", + "\n", + "

NPG Tracking Server

\n", + "

multiple folders found

\n
    \n", + (map{"
  • $_
    • \n"}@list), + "
\n\n" + or croak "Error printing: $ERRNO"; + return; +} + + sub _script_name { my $name = $PROGRAM_NAME; ($name) = $name =~ m{([^/?]+)\Z}smx; @@ -40,41 +53,36 @@ sub main { # Apache httpd server, this depends on whether mod-rewrite is enabled # in the server, the version of the server and the history of its updates. my $script_name = _script_name(); - my ($pathglob, $runfolder, $suffix) = $path_info =~ + my ($pathglob) = $path_info =~ m{ \A(?:(?:.+/)?$script_name)? # Optionally, the name of this script, # optionally prepended by some url, # neither of which we need to capture. /? # An occasional extra slash - ((?:/\S+?/\*)?) # Run folder path glob. - / - ([^/?]+) # Run folder name. - (.*) }smx; + (/[\/a-zA-Z0-9_*{},-]+?) # path glob. + \z + }smx; - if (!($pathglob && $runfolder)) { - _error('Failed to get pathglob or run folder or both', $path_info); + if (!($pathglob )) { + _error('Failed to get pathglob', $path_info); return; } - my @folders = sort { -M $a <=> -M $b } glob "$pathglob/$runfolder"; + my @folders = grep {length} # remove empty entries post-detaint + map { /([\/a-z0-9_-]+)/imsx ? $1 : q() } #detaint + sort { -M $a <=> -M $b } + glob $pathglob; if (!@folders) { - _error('Run folder not found', $path_info); + _error('Folder not found', $pathglob); return; } - my ($uri) = $folders[0]=~/([\/a-z0-9_-]+)/imsx; # detaint - if (!$uri) { - _error('Detainting has not left anything', $path_info); + if (@folders > 1) { + _list_folders(@folders); return; } - my $rellink = readlink "$uri/Latest_Summary"; - if (defined $rellink) { - $suffix =~ s{^/Latest_Summary}{/$rellink}smx; - } - - my $UNSAFE = q[#]; - $uri .= q(/) . uri_escape($suffix,$UNSAFE); + my $uri = $folders[0]; print "Content-type: text/html\n\n", qq(\n) diff --git a/lib/Monitor/RunFolder/Staging.pm b/lib/Monitor/RunFolder/Staging.pm index e339198a..3b6802b1 100644 --- a/lib/Monitor/RunFolder/Staging.pm +++ b/lib/Monitor/RunFolder/Staging.pm @@ -39,7 +39,10 @@ Readonly::Scalar my $DEFAULT_ONBOARD_ANALYSIS_DN => q[1]; # used at the moment. Readonly::Scalar my $ONBOARD_ANALYSIS_COMPLETE_FN => q[Secondary_Analysis_Complete.txt]; -Readonly::Scalar my $ONBOARD_ANALYSIS_SAMPLESHEET_FN => q[SampleSheet.csv]; + +Readonly::Array my @UPDATES_FOR_INCOMING_ALLOWED_STATUSES => + ('run pending', 'run in progress', 'run complete'); +Readonly::Scalar my $USERNAME => 'pipeline'; has 'status_update' => (isa => 'Bool', is => 'ro', @@ -93,27 +96,6 @@ sub is_run_complete { return $is_run_complete; } - - -sub is_onboard_analysis_planned { - my $self = shift; - - my $planned = 0; - if ($self->platform_NovaSeqX()) { - my $ss = join q[/], - $self->runfolder_path(), $ONBOARD_ANALYSIS_SAMPLESHEET_FN; - my $have_ss = -f $ss; - carp sprintf 'Samplesheet %s for the onboard analysis%sfound', - $ss, $have_ss ? q[ ] : q[ not ]; - if ($have_ss) { - $planned = any { $_ =~ /^\[BCLConvert/smx } read_file($ss); - carp sprintf 'Samplesheet %s %s the BCLConvert section', - $ss, $planned ? q[has] : q[doesn't have]; - } - } - return $planned; -} - sub is_onboard_analysis_output_copied { my $self = shift; @@ -352,6 +334,148 @@ sub _set_sgid { return; } +sub _log { + my @ms = map { "\t$_\n" } @_; + print {*STDOUT} @ms or carp $OS_ERROR; +} + + +sub update_run_from_path { ##### Method to deal with one run folder + my ($folder, $hash_previous_size_of,$inhibit_folder_move) = @_; # folder is like "self" - code converted from function "check_path" + my $run_path = $folder->runfolder_path; # in case path was transformed + + my $run_status = $folder->tracking_run()->current_run_status_description(); + my $id_run = $folder->tracking_run()->id_run; + + _log("Run $id_run status $run_status"); + if ($folder->platform_NovaSeqX()) { + _log("... run on NovaSeqX instrument"); + } + + my $db_flowcell_barcode = $folder->tracking_run()->flowcell_id; + my $staging_flowcell_barcode = $folder->run_flowcell; # from RunParameters.xml + $staging_flowcell_barcode ||= q[]; + if ($db_flowcell_barcode) { # database flowcell barcode validation + if ($db_flowcell_barcode ne $staging_flowcell_barcode) { + croak 'Flowcell barcode mismatch between database and staging: ' . + join q[ ], $db_flowcell_barcode, $staging_flowcell_barcode; + } + } else { # save flowcell barcode to the tracking database + $staging_flowcell_barcode or croak + "Staging flowcell barcode is not defined for run $id_run"; + _log("Saving staging flowcell barcode $staging_flowcell_barcode to the database."); + $folder->tracking_run()->update({flowcell_id => $staging_flowcell_barcode}); + } + + if ($folder->is_in_analysis) { + _log('Folder is in /analysis/'); + + if( $run_status eq 'qc complete') { + _log('Moving run folder to /outgoing/'); + (not $inhibit_folder_move) and _log($folder->move_to_outgoing()); + } + return; # Nothing else to do for a folder in /analysis/ + } + + _log('Folder is in /incoming/'); + + # If we don't remember seeing it before, set the folder name and glob; + # set staging tag, if appropriate, set/fix instrument side, workflow side. + # Previously we avoided making changes to the db if status was at or after + # 'run complete'. We might consider reinstating this rule. + if ( not defined $hash_previous_size_of->{$run_path} ) { + $folder->update_run_record(); + $folder->tracking_run()->set_tag( $USERNAME, 'staging' ); + _log('Set staging tag'); + try { + my $iside = $folder->set_instrument_side(); + if ($iside) { + _log("Instrument side is set to $iside"); + } + my $wf_type = $folder->set_workflow_type(); + if ($wf_type) { + _log("Workflow type is set to $wf_type"); + } + $folder->set_run_tags(); + } catch { + _log('Error: ' . $_); + }; + + $hash_previous_size_of->{$run_path} = 0; + } + + # Could delete the directory here. Leave it for now. + return if $run_status eq 'data discarded'; + + if (any { $run_status eq $_ } @UPDATES_FOR_INCOMING_ALLOWED_STATUSES) { + + my $latest_cycle = $folder->get_latest_cycle(); + if ($folder->update_cycle_count($latest_cycle)) { + _log("Cycle count updated to $latest_cycle"); + } + + if ( $run_status eq 'run pending' ) { + + if ($latest_cycle) { + $folder->update_run_status('run in progress'); + _log(q[Run status updated to 'run in progress']); + } + + } elsif ( $run_status eq 'run in progress' ) { + + # The lane count comes from the run folder structure, which + # we should have by now set up. + $folder->delete_superfluous_lanes(); + if ($folder->is_run_complete()) { + $folder->update_run_status('run complete'); + _log(q[Run status updated to 'run complete']); + } + + } else { # run status is 'run complete' + + $folder->update_run_record(); # Inspect and update cycles, + # including expected cycle count! + + if ( $folder->check_tiles($run_path) ) { + + my $previous_size = $hash_previous_size_of->{$run_path}; + my ( $current_size, $latest_mod ) = $folder->monitor_stats(); + _log(sprintf 'Run folder sizes: previous %i, current %i', + $previous_size, $current_size); + $hash_previous_size_of->{$run_path} = $current_size; + + if ( $current_size != $previous_size ) { + _log('Runfolder size is still changing.'); + return; + } + + # Check that no file is 'in the future'. + if ( $latest_mod > time ) { + _log("Files in 'future' $latest_mod are present."); + return; + } + + # Check if we are waiting for the onboard analysis to finish. + if ($folder->onboard_analysis_planned() && + !$folder->is_onboard_analysis_output_copied()) { + return; + } + + # Set status to 'run mirrored' and move run folder + # from /incoming/ to /analysis/ + $folder->update_run_status('run mirrored'); + _log(q[Run status updated to 'run mirrored']); + _log('Moving run folder to analysis'); + (not $inhibit_folder_move) and _log($folder->move_to_analysis()); + + return 'done'; + } + } + } + + return; + +} ###### End of method to deal with one run folder no Moose; __PACKAGE__->meta->make_immutable(); @@ -418,18 +542,24 @@ false otherwise. Move the run folder from 'analysis' to 'outgoing'. -=head2 is_onboard_analysis_planned - -Returns true if the run folder for the NovaSeq SeriesX run contains a -samplesheet with a section for the bcl on board data conversion. Always returns -false for other instrument types. - =head2 is_onboard_analysis_output_copied Returns true if the file that flags the end of the transfer of the onboard analysis output to staging is present in the default DRAGEN analysis directory ([RUNFOLDER_NAME]/Analysis/1/ at the moment). +=head2 update_run_from_path + + C<<$folder->update_run_from_path($hash_ref_runfolder_size_state_store, + $inhibit_folder_move);>> + +Uses information found in the runfolder, dependent on its location, to update +the tracking database. Your'll need to trace the code for the exact logic... +It will also move the run folder until the flag to inhibit this is passed. +It takes a hash ref contain the (size) state of run folders - this is (in some +logical paths) used to help determine whether certain processes have +completed. + =head1 CONFIGURATION AND ENVIRONMENT =head1 DEPENDENCIES diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm new file mode 100644 index 00000000..3a4b479d --- /dev/null +++ b/lib/npg/samplesheet/auto.pm @@ -0,0 +1,267 @@ +package npg::samplesheet::auto; + +use Moose; +use namespace::autoclean; +use Try::Tiny; +use File::Basename; +use Readonly; +use File::Copy; +use File::Spec::Functions; + +use npg::samplesheet; +use npg_tracking::Schema; +use WTSI::DNAP::Warehouse::Schema; +use st::api::lims; +use st::api::lims::samplesheet; + +with q(MooseX::Log::Log4perl); + +our $VERSION = '0'; + +Readonly::Scalar my $DEFAULT_SLEEP => 90; + +=head1 NAME + +npg::samplesheet::auto + +=head1 VERSION + +=head1 SYNOPSIS + + use npg::samplesheet::auto; + use Log::Log4perl qw(:easy); + BEGIN{ Log::Log4perl->easy_init({level=>$INFO,}); } + npg::samplesheet::auto->new()->loop(); + +=head1 DESCRIPTION + +Class for creating Illumina MiSeq samplesheets automatically +for runs which are pending. + +=head1 SUBROUTINES/METHODS + +=head2 npg_tracking_schema + +=cut + +has 'npg_tracking_schema' => ( + 'isa' => 'npg_tracking::Schema', + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build_npg_tracking_schema { + return npg_tracking::Schema->connect(); +} + +=head2 mlwh_schema + +=cut + +has 'mlwh_schema' => ( + 'isa' => 'WTSI::DNAP::Warehouse::Schema', + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build_mlwh_schema { + return WTSI::DNAP::Warehouse::Schema->connect(); +} + +=head2 sleep_interval + +=cut + +has 'sleep_interval' => ( + 'is' => 'ro', + 'isa' => 'Int', + 'default' => $DEFAULT_SLEEP, +); + +=head2 loop + +Repeat the process step with the intervening sleep interval. + +=cut + +sub loop { + my $self = shift; + while(1) { $self->process(); sleep $self->sleep_interval;} + return; +}; + +=head2 process + +Find all pending MiSeq runs and create an Illumina samplesheet for each +of them if one does not already exist. + +=cut + +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[ runs marked as ] .($self->_pending->description)); + while(my$r=$rs->next){ + my $id_run = $r->id_run; + $self->log->info('Considering ' . join q[,],$id_run,$r->instrument->name); + + my $l = st::api::lims->new( + position => 1, + id_run => $id_run, + id_flowcell_lims => $r->batch_id, + driver_type => q(ml_warehouse), + mlwh_schema => $self->mlwh_schema + ); + + my $ss = npg::samplesheet->new(run => $r, lims => [$l]); + + 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); + } + } + + if ($generate_new) { + try { + $ss->process; + $self->log->info(qq($o created for run ).($r->id_run)); + } catch { + $self->log->error(qq(Trying to create $o for run ).($r->id_run). + qq( experienced error: $_)); + } + } + } + return; +} + +has '_miseq' => ( + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build__miseq { + my $self=shift; + return $self->npg_tracking_schema->resultset(q(InstrumentFormat)) + ->find({q(model)=>q(MiSeq)}); +} + +has '_pending' => ( + 'is' => 'ro', + 'lazy_build' => 1, +); +sub _build__pending { + my $self=shift; + return $self->npg_tracking_schema->resultset(q(RunStatusDict)) + ->find({q(description)=>q(run pending)}); +} + +sub _id_run_from_samplesheet { + my $file_path = shift; + my $id_run; + try { + my $sh = st::api::lims::samplesheet->new(path => $file_path); + $sh->data; # force to parse the file + if ($sh->id_run) { + $id_run = int $sh->id_run; + } + }; + return $id_run; +} + +sub _move_samplesheet { + my $file_path = shift; + + my($filename, $dirname) = fileparse($file_path); + $dirname =~ s/\/$//smx; #drop last forward slash if any + my $dirname_dest = $dirname . '_old'; + my $filename_dest = $filename . '_invalid'; + my $moved; + if (-d $dirname_dest) { + $moved = move($file_path, catdir($dirname_dest, $filename_dest)); + } + if (!$moved) { + move($file_path, catdir($dirname, $filename_dest)); + } + return; +} + +__PACKAGE__->meta->make_immutable; + +1; + +__END__ + +=head1 DIAGNOSTICS + +=head1 CONFIGURATION AND ENVIRONMENT + +=head1 DEPENDENCIES + +=over + +=item File::Basename + +=item File::Copy + +=item Moose + +=item namespace::autoclean + +=item MooseX::Log::Log4perl + +=item Readonly + +=item File::Spec::Functions + +=item Try::Tiny + +=item npg_tracking::Schema + +=item npg::samplesheet + +=item st:api::lims + +=item st::api::lims::samplesheet + +=item WTSI::DNAP::Warehouse::Schema + +=back + +=head1 INCOMPATIBILITIES + +=head1 BUGS AND LIMITATIONS + +=head1 AUTHOR + +David K. Jackson Edavid.jackson@sanger.ac.ukE + +=head1 LICENSE AND COPYRIGHT + +Copyright (C) 2012,2013,2014,2019,2021,2023 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/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index 5981d6c9..bbdabd79 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -66,7 +66,7 @@ on this instrument model. The DRAGEN analysis can process a limited number of distinct analysis configurations. The germline and RNA alignment sections of the generated -samplesheet will contain as many samples as possible within the limit set by +samplesheet will contain as many samples as possible within the limit set by the C attribute. The default value for this attribute is 4, which is the number of distinct configurations that the on-board DRAGEN analysis can handle. @@ -74,10 +74,10 @@ on-board DRAGEN analysis can handle. In the BCLConvert section, each combination of index lengths counts as a unique configuration. If the number of these configurations exceeds the value of the the C attribute, no DRAGEN analysis -sections are added to the samplesheet. +sections are added to the samplesheet. See specification in -L +L A full listing of analysis options is available in L @@ -171,7 +171,7 @@ has 'keep_fastq' => ( Variant calling mode, defaults to C, other valid options are C and C - + =cut has 'varcall' => ( @@ -306,8 +306,10 @@ sub _build_run_name { my $run_name; if ($self->has_id_run()) { - $run_name = $self->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; } else { + # Run is not tracked, generate a placeholder ID my $ug = Data::UUID->new(); my @a = split /-/xms, $ug->to_string($ug->create()); # Add a random string at the end so that the batch can be reused. @@ -333,21 +335,14 @@ sub _build_file_name { my $file_name; if ($self->has_id_run) { - my $side = $self->run->is_tag_set('fc_slotA') ? 'A' : - ($self->run->is_tag_set('fc_slotB') ? 'B' : q[]); - if (!$side) { - croak 'Slot is not set for run ' . $self->id_run; - } $file_name = join q[_], - $self->run->instrument->name, - $self->id_run, - $side, + $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 + 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; @@ -642,7 +637,7 @@ sub add_common_headers { $self->_add_line(qw(InstrumentType NovaSeqXPlus)); $self->_add_line(); - # Reads section + # Reads section $self->_add_line('[Reads]'); $self->_add_line(q[Read1Cycles], $READ1_LENGTH); $self->_add_line(q[Read2Cycles], $READ2_LENGTH); @@ -695,6 +690,24 @@ 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 +intended to be inserted into. Croaks when no value has been set. + +=cut + +sub get_instrument_side { + my $self = shift; + my $side = $self->run->is_tag_set('fc_slotA') ? 'A' : + ($self->run->is_tag_set('fc_slotB') ? 'B' : q[]); + if (! $side) { + croak 'Slot is not set for run ' . $self->id_run; + } + return $side; +} + + sub _add_samples { my ($self, @samples) = @_; diff --git a/lib/npg_tracking/illumina/run/long_info.pm b/lib/npg_tracking/illumina/run/long_info.pm index a041669b..abe2e2ab 100644 --- a/lib/npg_tracking/illumina/run/long_info.pm +++ b/lib/npg_tracking/illumina/run/long_info.pm @@ -814,6 +814,22 @@ sub instrument_side { _get_single_element_text($self->_run_params(), 'FCPosition'); } +=head2 onboard_analysis_planned + +Returns true if the RunParameter.xml file contains a section indicating +that DRAGEN analysis is planned, returns false otherwise. Of all locally +available sequencing instruments, ony NovaSeqX instruments are expected +to have this section. + +=cut + +sub onboard_analysis_planned { + my $self = shift; + my $workflows = _get_single_element_text( + $self->_run_params(), 'SecondaryAnalysisWorkflow'); + return $workflows && ($workflows =~ /DRAGEN/xms); +} + ######################################################### # Private attributes # ######################################################### @@ -986,7 +1002,8 @@ sub _get_xml_document { croak 'Directory path required'; } - my @files = grep { m/\/$reg_expr\Z/xms } io($dir)->all; + my @files = grep { m/\/$reg_expr\Z/xms } io("$dir/")->all; + # "/" suffix of $dir/ to cope with a symlink for a run folder if (@files < 1) { croak qq{File not found for $reg_expr in $dir}; } diff --git a/lib/npg_tracking/illumina/run/short_info.pm b/lib/npg_tracking/illumina/run/short_info.pm index 25353cc6..5e08a2a4 100644 --- a/lib/npg_tracking/illumina/run/short_info.pm +++ b/lib/npg_tracking/illumina/run/short_info.pm @@ -95,8 +95,10 @@ sub _build_id_run { $self->run_folder(); } + # Try to read id_run from the folder name ($inst_t, $inst_i, $id_run) = $self->run_folder() =~ /$NAME_PATTERN/gmsx; + # Failing that try the tracking DB. if ( !$id_run ) { if ($self->can(q(npg_tracking_schema)) and $self->npg_tracking_schema()) { my $rs = $self->npg_tracking_schema()->resultset('Run') @@ -107,8 +109,18 @@ sub _build_id_run { } } + # When no id_run is set (as in pick-up runs) attempt to parse an id_run from + # the experiment name recorded in the Illumina XML file. + # We embed additional information in NovaSeqX samplesheets which have no + # meaning here. See L if ( !$id_run && $self->can('experiment_name') && $self->experiment_name() ) { - ($id_run) = $self->experiment_name() =~ /\A[\s]*([\d]+)[\s]*\Z/xms; + ($id_run, undef) = $self->experiment_name() =~ m{ + \A + [\s]* + ([\d]+) # id_run + ([\w\d\s]*) # instrument name or other embedded info + \Z + }xms; } if( !$id_run ) { diff --git a/t/10-transcriptome.t b/t/10-transcriptome.t index 896cc5bb..2f47293f 100644 --- a/t/10-transcriptome.t +++ b/t/10-transcriptome.t @@ -6,229 +6,180 @@ use File::Spec::Functions qw(catfile); use Test::Exception; use File::Temp qw/ tempdir /; use File::Path qw/make_path/; -use File::chdir; -use File::Copy; -use Cwd; -use Carp; -use IO::File; +use Moose::Meta::Class; use st::api::lims; -my $repos = 't/data/repos1'; - use_ok('npg_tracking::data::transcriptome'); -{ my $tmp_repos = tempdir( CLEANUP => 1); -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = $tmp_repos; +my $dir = join q[/],$tmp_repos,'transcriptomes'; my %builds = (); - $builds{'Homo_sapiens'} = ['1000Genomes_hs37d5','CGP_GRCh37.NCBI.allchr_MT','GRCh37_53']; - $builds{'Mus_musculus'} = ['GRCm38','NCBIm37','std_unmasked_NCBIm37']; - -my $dir = join q[/],$tmp_repos,'transcriptomes'; +$builds{'Homo_sapiens'} = ['1000Genomes_hs37d5','CGP_GRCh37.NCBI.allchr_MT','GRCh37_53']; +$builds{'Mus_musculus'} = ['GRCm38','NCBIm37','std_unmasked_NCBIm37']; foreach my $spp (keys %builds){ - my $rel_dir1 = join q[/],$dir,$spp,'ensembl_75_transcriptome'; - my $rel_dir2 = join q[/],$dir,$spp,'ensembl_74_transcriptome'; - my $rel_dir3 = join q[/],$dir,$spp,'ensembl_84_transcriptome'; - - foreach my $rel_dir ($rel_dir1,$rel_dir2,$rel_dir3){ - - foreach my $build (@{ $builds{$spp} }){ - my $gtf_dir = join q[/],$rel_dir,$build,'gtf'; - my $rnaseq_dir = join q[/],$rel_dir,$build,'RNA-SeQC'; - my $tophat_dir = join q[/],$rel_dir,$build,'tophat2'; - my $salmon_dir = join q[/],$rel_dir,$build,'salmon'; - my $fasta_dir = join q[/],$rel_dir,$build,'fasta'; - my $globin_dir = join q[/],$rel_dir,$build,'globin'; - my $mt_dir = join q[/],$rel_dir,$build,'mt'; - make_path($gtf_dir, - $rnaseq_dir, - $tophat_dir, - $salmon_dir, - $fasta_dir, - $globin_dir, - $mt_dir, - {verbose => 0}); - } - } - - #symlink_default($dir,$spp,'ensembl_75_transcriptome'); - + my $rel_dir1 = join q[/],$dir,$spp,'ensembl_75_transcriptome'; + my $rel_dir2 = join q[/],$dir,$spp,'ensembl_74_transcriptome'; + my $rel_dir3 = join q[/],$dir,$spp,'ensembl_84_transcriptome'; + + foreach my $rel_dir ($rel_dir1,$rel_dir2,$rel_dir3){ + foreach my $build (@{ $builds{$spp} }){ + my $gtf_dir = join q[/],$rel_dir,$build,'gtf'; + my $rnaseq_dir = join q[/],$rel_dir,$build,'RNA-SeQC'; + my $tophat_dir = join q[/],$rel_dir,$build,'tophat2'; + my $salmon_dir = join q[/],$rel_dir,$build,'salmon'; + my $fasta_dir = join q[/],$rel_dir,$build,'fasta'; + my $globin_dir = join q[/],$rel_dir,$build,'globin'; + my $mt_dir = join q[/],$rel_dir,$build,'mt'; + make_path($gtf_dir, + $rnaseq_dir, + $tophat_dir, + $salmon_dir, + $fasta_dir, + $globin_dir, + $mt_dir, + {verbose => 0}); + } + } } -my $batch_dir = join q[/],'st','batches'; -my $samples_dir = join q[/],'st','samples'; -my $study_dir = join q[/],'st','studies'; - -make_path ("$tmp_repos/$batch_dir","$tmp_repos/$samples_dir","$tmp_repos/$study_dir",{verbose => 0}); #to create directory tree - -#Mouse -copy("$repos/$batch_dir/25539.xml","$tmp_repos/$batch_dir/25539.xml") or carp "Copy failed: $!"; -copy("$repos/$samples_dir/1807468.xml","$tmp_repos/$samples_dir/1807468.xml") or carp "Copy failed: $!"; -#Human -copy("$repos/$batch_dir/25715.xml","$tmp_repos/$batch_dir/25715.xml") or carp "Copy failed: $!"; -copy("$repos/$samples_dir/1830658.xml","$tmp_repos/$samples_dir/1830658.xml") or carp "Copy failed: $!"; -copy("$repos/$study_dir/2910.xml","$tmp_repos/$study_dir/2910.xml") or carp "Copy failed: $!"; - -#make directory structure with empty files +# Make directory structure with empty files my @files = (); -$files[0] = join(q[/], $dir, 'Mus_musculus','ensembl_75_transcriptome', 'GRCm38','gtf','ensembl_75_transcriptome-GRCm38.gtf'); +$files[0] = join(q[/], $dir, 'Mus_musculus','ensembl_75_transcriptome', + 'GRCm38','gtf','ensembl_75_transcriptome-GRCm38.gtf'); foreach my $v ('ensembl_74_transcriptome','ensembl_75_transcriptome'){ - my $vdir = join(q[/], $dir, 'Homo_sapiens',$v, '1000Genomes_hs37d5',); - push @files, join(q[/], $vdir,'gtf',$v . '-1000Genomes_hs37d5.gtf'); - push @files, join(q[/], $vdir,'RNA-SeQC',$v . '-1000Genomes_hs37d5.gtf'); - push @files, join(q[/], $vdir,'tophat2','1000Genomes_hs37d5.known.1.bt2'); - push @files, join(q[/], $vdir,'tophat2','1000Genomes_hs37d5.known.ver'); - push @files, join(q[/], $vdir,'salmon','versionInfo.json'); - push @files, join(q[/], $vdir,'salmon','refInfo.json'); - push @files, join(q[/], $vdir,'salmon','header.json'); - push @files, join(q[/], $vdir,'fasta','1000Genomes_hs37d5.fa'); - push @files, join(q[/], $vdir,'globin','globin_genes.csv'); - push @files, join(q[/], $vdir,'mt','mt_genes.csv'); + my $vdir = join(q[/], $dir, 'Homo_sapiens',$v, '1000Genomes_hs37d5',); + push @files, join(q[/], $vdir,'gtf',$v . '-1000Genomes_hs37d5.gtf'); + push @files, join(q[/], $vdir,'RNA-SeQC',$v . '-1000Genomes_hs37d5.gtf'); + push @files, join(q[/], $vdir,'tophat2','1000Genomes_hs37d5.known.1.bt2'); + push @files, join(q[/], $vdir,'tophat2','1000Genomes_hs37d5.known.ver'); + push @files, join(q[/], $vdir,'salmon','versionInfo.json'); + push @files, join(q[/], $vdir,'salmon','refInfo.json'); + push @files, join(q[/], $vdir,'salmon','header.json'); + push @files, join(q[/], $vdir,'fasta','1000Genomes_hs37d5.fa'); + push @files, join(q[/], $vdir,'globin','globin_genes.csv'); + push @files, join(q[/], $vdir,'mt','mt_genes.csv'); } -#make directory structure with empty files and funny business (multiple files, missing files, etc) +# Make directory structure with empty files and funny business +# (multiple files, missing files, etc) foreach my $v ('ensembl_84_transcriptome'){ - my $vdir = join(q[/], $dir, 'Mus_musculus',$v, 'GRCm38',); - #more than 1 gtf present - push @files, join(q[/], $vdir,'gtf',$v . '-GRCm38.gtf'); - push @files, join(q[/], $vdir,'gtf', 'GRCm38_sans_mt.gtf'); - #the rest of the instances are missing + my $vdir = join(q[/], $dir, 'Mus_musculus',$v, 'GRCm38',); + #more than 1 gtf present + push @files, join(q[/], $vdir,'gtf',$v . '-GRCm38.gtf'); + push @files, join(q[/], $vdir,'gtf', 'GRCm38_sans_mt.gtf'); + #the rest of the instances are missing } foreach my $file (@files){ `touch $file`; } -########################################################################################################################### -#Mus_musculus (GRCm38 + ensembl_75_transcriptome) Transcriptome Analysis -my %init = (id_run => 12071, position => 4, tag_index => 2); -my $m_test = npg_tracking::data::transcriptome->new (%init, - lims => st::api::lims->new(%init, batch_id => 25539, driver_type => 'xml'), - repository => $tmp_repos, aligner => 'tophat2'); -isa_ok($m_test, 'npg_tracking::data::transcriptome'); -lives_and { is basename($m_test->gtf_file), 'ensembl_75_transcriptome-GRCm38.gtf' } 'file ensembl_75_transcriptome-GRCm38.gtf found'; +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_transcriptome] +); +my %driver_info = (driver_type => 'ml_warehouse', mlwh_schema => $schema_wh); +############################################################################## -#Homo_sapiens (1000Genomes_hs37d5) -%init = (id_run => 12161, position => 1, tag_index => 1); + +# Homo_sapiens (1000Genomes_hs37d5) +my %init = (id_run => 12161, position => 1, tag_index => 1); my $test = npg_tracking::data::transcriptome->new (%init, - lims => st::api::lims->new(%init, batch_id => 25715, driver_type => 'xml'), + lims => st::api::lims->new(%init, id_flowcell_lims => 25715, %driver_info), repository => $tmp_repos); - -lives_and { is $test->transcriptome_index_path,undef } "ok - returns undef for transcriptome_index_path if no transcriptome version in reference name - Homo_sapiens (1000Genomes_hs37d5)"; - -##update sample xml so that Reference Genome is missing (study 2910.xml already has this field empty) -copy("$tmp_repos/$samples_dir/1830658.xml", "$tmp_repos/$samples_dir/1830658.xml.1") or carp "Copy failed: $!"; -my $fh = IO::File->new("<$tmp_repos/$samples_dir/1830658.xml.1") or carp "cannot open $repos/$samples_dir/1830658.xml.1"; -my $w_fh = IO::File->new(">$tmp_repos/$samples_dir/1830658.xml") or carp "cannot open $repos/$samples_dir/1830658.xml"; -while(<$fh>){ - if (/Homo_sapiens\s+(\S+)/){ - print $w_fh " " x 6 . "\n"; - } - else { print $w_fh $_ } -} -$w_fh->close; -$fh->close; - -%init = (id_run => 12161, position => 1, tag_index => 1); +isa_ok($test, 'npg_tracking::data::transcriptome'); +lives_and { is $test->transcriptome_index_path, undef } + "undef for transcriptome_index_path if no transcriptome version in reference"; + +# Update sample data so that Reference Genome is undefined +# (study 2910 already has this field empty) +my $sample_rs = $schema_wh->resultset('Sample'); +$sample_rs->search({id_sample_lims => 1830658})->next + ->update({reference_genome => undef}); my $test2 = npg_tracking::data::transcriptome->new (%init, - lims => st::api::lims->new(%init, batch_id => 25715, driver_type => 'xml'), + lims => st::api::lims->new(%init, id_flowcell_lims => 25715, %driver_info), repository => $tmp_repos); -lives_and { is $test2->transcriptome_index_path, undef } "no path for bowtie2 indices found (reference genome missing in sample and study xml)"; - - -##update sample xml so that Reference Genome has a transcriptome version : Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome) +lives_and { is $test2->transcriptome_index_path, undef } + "no path for bowtie2 indices found (reference genome is undefined)"; -my $ver_fh = IO::File->new("<$tmp_repos/$samples_dir/1830658.xml.1") or carp "cannot open $repos/$samples_dir/1830658.xml.1"; -my $ver_w_fh = IO::File->new(">$tmp_repos/$samples_dir/1830658.xml") or carp "cannot open $repos/$samples_dir/1830658.xml"; -while(<$ver_fh>){ - if (/Homo_sapiens\s+(\S+)/){ - print $ver_w_fh " " x 6 . "Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)\n"; - } - else { print $ver_w_fh $_ } -} -$ver_w_fh->close; -$ver_fh->close; - -%init = (id_run => 12161, position => 1, tag_index => 1); +# Update sample reference genome. +$sample_rs->search({id_sample_lims => 1830658})->next->update({ + reference_genome => q[Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)]}); my $test3 = npg_tracking::data::transcriptome->new (%init, - lims => st::api::lims->new(%init, batch_id => 25715, driver_type => 'xml'), + lims => st::api::lims->new(%init, id_flowcell_lims => 25715, %driver_info), repository => $tmp_repos); -lives_and { is basename($test3->gtf_file), 'ensembl_74_transcriptome-1000Genomes_hs37d5.gtf' } 'file ensembl_74_transcriptome-1000Genomes_hs37d5.gtf found where reference = Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)'; - -lives_and { is basename($test3->rnaseqc_gtf_file), 'ensembl_74_transcriptome-1000Genomes_hs37d5.gtf' } 'RNA-SeQC file ensembl_74_transcriptome-1000Genomes_hs37d5.gtf found where reference = Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)'; - -lives_and { is $test3->transcriptome_index_path, catfile($tmp_repos, q[transcriptomes/Homo_sapiens/ensembl_74_transcriptome/1000Genomes_hs37d5/tophat2]) +lives_and { is basename($test3->gtf_file), + 'ensembl_74_transcriptome-1000Genomes_hs37d5.gtf' } + 'file ensembl_74_transcriptome-1000Genomes_hs37d5.gtf found'; +lives_and { is basename($test3->rnaseqc_gtf_file), + 'ensembl_74_transcriptome-1000Genomes_hs37d5.gtf' } + 'RNA-SeQC file ensembl_74_transcriptome-1000Genomes_hs37d5.gtf found'; +lives_and { is $test3->transcriptome_index_path, + catfile($tmp_repos, + q[transcriptomes/Homo_sapiens/ensembl_74_transcriptome/1000Genomes_hs37d5/tophat2]) } "correct path for bowtie2 indices found"; - -lives_and { is basename($test3->globin_file), 'globin_genes.csv' } 'globin genes csv file found where reference = Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)'; - -lives_and { is basename($test3->mt_file), 'mt_genes.csv' } 'mt genes csv file found where reference = Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)'; - -my $prefix_path_74 = catfile($tmp_repos, q[transcriptomes/Homo_sapiens/ensembl_74_transcriptome/1000Genomes_hs37d5/tophat2/1000Genomes_hs37d5.known]); -lives_and { is $test3->transcriptome_index_name, $prefix_path_74 } "Correctly found transcriptome version index name path and prefix "; +lives_and { is basename($test3->globin_file), 'globin_genes.csv' } + 'globin genes csv file found'; +lives_and { is basename($test3->mt_file), 'mt_genes.csv' } + 'mt genes csv file found'; +my $prefix_path_74 = catfile($tmp_repos, + q[transcriptomes/Homo_sapiens/ensembl_74_transcriptome/1000Genomes_hs37d5/tophat2/1000Genomes_hs37d5.known]); +lives_and { is $test3->transcriptome_index_name, $prefix_path_74 } + "Correctly found transcriptome version index name path and prefix "; my $test4 = npg_tracking::data::transcriptome->new ( %init, repository => $tmp_repos, - lims => st::api::lims->new(%init, batch_id => 25715, driver_type => 'xml'), + lims => st::api::lims->new(%init, id_flowcell_lims => 25715, %driver_info), aligner => 'tophat2', analysis => 'salmon'); -lives_and { is $test4->transcriptome_index_path, catfile($tmp_repos, q[transcriptomes/Homo_sapiens/ensembl_74_transcriptome/1000Genomes_hs37d5/salmon]) +lives_and { is $test4->transcriptome_index_path, catfile($tmp_repos, + q[transcriptomes/Homo_sapiens/ensembl_74_transcriptome/1000Genomes_hs37d5/salmon]) } "correct path for salmon indices found"; - lives_and { is $test4->transcriptome_index_name, undef } "ok - returns undef when looking for index name for salmon"; my $test5 = npg_tracking::data::transcriptome->new ( %init, repository => $tmp_repos, - lims => st::api::lims->new(%init, batch_id => 25715, driver_type => 'xml') + lims => st::api::lims->new(%init, id_flowcell_lims => 25715, %driver_info) ); lives_and { is basename($test5->fasta_file), '1000Genomes_hs37d5.fa' -} "transcriptome fasta file 1000Genomes_hs37d5.fa found where reference = Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)"; +} "transcriptome fasta file 1000Genomes_hs37d5.fa found"; +# Mus_musculus +%init = (id_run => 12071, position => 4, tag_index => 2); -##update sample xml so that Reference Genome has a transcriptome version : Mus_musculus (GRCm38 + ensembl_84_transcriptome) -copy("$tmp_repos/$samples_dir/1807468.xml", "$tmp_repos/$samples_dir/1807468.xml.1") or carp "Copy failed: $!"; -my $cpy_fh = IO::File->new("<$tmp_repos/$samples_dir/1807468.xml.1") or carp "cannot open $repos/$samples_dir/1807468.xml.1"; -my $mm_ver_fh = IO::File->new(">$tmp_repos/$samples_dir/1807468.xml") or carp "cannot open $repos/$samples_dir/1807468.xml"; -while(<$cpy_fh>){ - if (/Mus_musculus\s+(\S+)/){ - print $mm_ver_fh " " x 6 . "Mus_musculus (GRCm38 + ensembl_84_transcriptome)\n"; - } - else { print $mm_ver_fh $_ } -} -$mm_ver_fh->close; -$cpy_fh->close; +# Update sample reference genome +$sample_rs->search({id_sample_lims => 1807468})->next->update({ + reference_genome => q[Mus_musculus (GRCm38 + ensembl_75_transcriptome)]}); +my $test7 = npg_tracking::data::transcriptome->new (%init, + lims => st::api::lims->new(%init, id_flowcell_lims => 25539, %driver_info), + repository => $tmp_repos, aligner => 'tophat2'); +lives_and { is basename($test7->gtf_file), 'ensembl_75_transcriptome-GRCm38.gtf' } + 'file ensembl_75_transcriptome-GRCm38.gtf found'; -%init = (id_run => 12071, position => 4, tag_index => 2); +# Update sample reference genome +$sample_rs->search({id_sample_lims => 1807468})->next->update({ + reference_genome => q[Mus_musculus (GRCm38 + ensembl_84_transcriptome)]}); my $test6 = npg_tracking::data::transcriptome->new ( %init, repository => $tmp_repos, - lims => st::api::lims->new(%init, batch_id => 25539, driver_type => 'xml')); + lims => st::api::lims->new(%init, id_flowcell_lims => 25539, %driver_info)); throws_ok { $test6->gtf_file } qr/More than one gtf file/, -'ok - croaks when more than 1 gtf file found - Mus_musculus (GRCm38 + ensembl_84_transcriptome)'; - -my $prefix_path_84 = catfile($tmp_repos, q[transcriptomes/Mus_musculus/ensembl_84_transcriptome/GRCm38/tophat2/GRCm38.known]); +'ok - error when more than 1 gtf file found'; +my $prefix_path_84 = catfile($tmp_repos, + q[transcriptomes/Mus_musculus/ensembl_84_transcriptome/GRCm38/tophat2/GRCm38.known]); my $re_no_idx_name = qr/^Directory.*exists.*index.*files.*not.*found.*$/msxi; my $empty_idx_name = $test6->transcriptome_index_name; -lives_and { is $empty_idx_name, undef } "ok - returns undef for transcriptome_index_name if index files are not present - Mus_musculus (GRCm38 + ensembl_84_transcriptome)"; +lives_and { is $empty_idx_name, undef } + "returns undef for transcriptome_index_name if index files are not present"; my ($tmsg, $msg); $tmsg = $test6->messages()->mlist; -foreach my $m (@{$tmsg}){ $msg = $m; last if ($msg =~ /$re_no_idx_name/); } -like($msg, $re_no_idx_name, 'ok - message stored when index files not found'); - +foreach my $m (@{$tmsg}){ + $msg = $m; last if ($msg =~ /$re_no_idx_name/); } +like($msg, $re_no_idx_name, 'ok - message stored when index files not found'); -# make default symlink -sub symlink_default { - my($dir,$spp,$release) = @_; - my $orig_dir = getcwd(); - my $rel_dir = join q[/],$dir,$spp; - chdir qq[$rel_dir]; - eval { symlink($release,"default") }; - print "symlink error $@" if $@; - chdir $orig_dir; - return; -} +1; diff --git a/t/34-monitor-runfolder-staging.t b/t/34-monitor-runfolder-staging.t index 971c741b..b60dab4a 100644 --- a/t/34-monitor-runfolder-staging.t +++ b/t/34-monitor-runfolder-staging.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 51; +use Test::More tests => 50; use Test::Exception; use Test::Warn; use File::Copy; @@ -465,7 +465,7 @@ subtest 'run completion for NovaSeqX' => sub { }; subtest 'onboard analysis completion for NovaSeqX' => sub { - plan tests => 8; + plan tests => 6; my $tmpdir = tempdir( CLEANUP => 1 ); copy('t/data/run_params/RunParameters.novaseqx.xml',"$tmpdir/RunParameters.xml") @@ -475,30 +475,20 @@ subtest 'onboard analysis completion for NovaSeqX' => sub { my $monitor = Monitor::RunFolder::Staging->new(runfolder_path => $tmpdir); - ok (!$monitor->is_onboard_analysis_planned(), + ok (!$monitor->onboard_analysis_planned(), 'onboard analysis is not planned'); ok (!$monitor->is_onboard_analysis_output_copied(), 'onboard analysis has not been copied'); - my $ss_file = "$tmpdir/SampleSheet.csv"; - open my $fh, '>', $ss_file or die 'Cannot open a file for writing'; - print $fh "[Header]\n[Cloud_BCLConvert_Settings]\n" or die 'Cannot print'; - close $fh or die 'Cannot close the file handle'; - ok (!$monitor->is_onboard_analysis_planned(), - 'onboard analysis is not planned'); - + copy('t/data/run_params/RunParameters.novaseqx.onboard.xml', + "$tmpdir/RunParameters.xml") or die "Copy failed: $!"; my $adir = "$tmpdir/Analysis"; mkdir $adir; + $monitor = Monitor::RunFolder::Staging->new(runfolder_path => $tmpdir); + ok ($monitor->onboard_analysis_planned(), 'onboard analysis is planned'); ok (!$monitor->is_onboard_analysis_output_copied(), 'onboard analysis has not been copied'); - - open $fh, '>>', $ss_file or die 'Cannot open a file for appending'; - print $fh "[BCLConvert_Settings]\n" or die 'Cannot print'; - close $fh or die 'Cannot close the file handle'; - ok ($monitor->is_onboard_analysis_planned(), 'onboard analysis is planned'); - ok (!$monitor->is_onboard_analysis_output_copied(), - 'onboard analysis has not been copied'); - + mkdir "$adir/2"; `touch $adir/2/CopyComplete.txt`; ok (!$monitor->is_onboard_analysis_output_copied(), @@ -510,26 +500,4 @@ subtest 'onboard analysis completion for NovaSeqX' => sub { 'onboard analysis has been copied'); }; -subtest 'no onboard analysis planned for NovaSeq' => sub { - plan tests => 2; - - my $tmpdir = tempdir( CLEANUP => 1 ); - copy('t/data/run_params/RunParameters.novaseq.xml',"$tmpdir/RunParameters.xml") - or die "Copy failed: $!"; - copy('t/data/run_info/runInfo.novaseq.xml',"$tmpdir/RunInfo.xml") - or die "Copy failed: $!"; - my $monitor = Monitor::RunFolder::Staging->new(runfolder_path => $tmpdir); - - ok (!$monitor->is_onboard_analysis_planned(), - 'onboard analysis is not planned'); - - my $ss_file = "$tmpdir/SampleSheet.csv"; - open my $fh, '>', $ss_file or die 'Cannot open a file for writing'; - print $fh "[Header]\n[BCLConvert_Settings]\n" or die 'Cannot print'; - close $fh or die 'Cannot close the file handle'; - ok (!$monitor->is_onboard_analysis_planned(), - 'onboard analysis is not planned'); -}; - - 1; diff --git a/t/35-monitor_one_runfolder.t b/t/35-monitor_one_runfolder.t new file mode 100644 index 00000000..b572d6a9 --- /dev/null +++ b/t/35-monitor_one_runfolder.t @@ -0,0 +1,280 @@ +use strict; +use warnings; +use Test::More tests => 7; +use Test::Exception; +use File::Path qw/make_path/; +use File::Copy; +use File::Temp qw/ tempdir /; + +use t::dbic_util; + +use_ok('Monitor::RunFolder::Staging'); + +######### +# Tests for high-level functionality, ie the update_run_from_path method +# of the Monitor::RunFolder::Staging class. In these tests the class +# instances are created the same way as in the staging_area_monitor script, +# i.e. by supplying the runfolder_path and npg_tracking_schema attributes. +# +# Tests are arranged roughly in the way the code flows. Each subtest +# corresponds to one loop of the staging monitor. +# + +my $schema = t::dbic_util->new->test_schema(); # t/data/dbic_fixtures +my $dir = tempdir( CLEANUP => 1 ); + +my $idir = "$dir/incoming"; +my $adir = "$dir/analysis"; +my $odir = "$dir/outgoing"; +make_path($idir, $adir, $odir); + +# Create bare-bones NovaSeqXPlus run. +my $id_run = 47539; +my $run = $schema ->resultset('Run')->create({ + id_run => $id_run, + expected_cycle_count => 8, + actual_cycle_count => 0, + id_instrument => 70, + id_instrument_format => 13, + team => 'A' +}); +$run->update_run_status('run pending'); + +my $runfolder_name = q[20230628_LH00210_0008_B225TGJLT3]; +# The runfolder is originally in 'incoming' +my $runfolder_path = join q[/], $idir, $runfolder_name; +make_path($runfolder_path); +my $basecalls_path = "$runfolder_path/Data/Intensities/BaseCalls"; + +copy 't/data/test_staging_daemon/novaseqxplus/RunInfo.xml', + "$runfolder_path/RunInfo.xml"; +copy 't/data/test_staging_daemon/novaseqxplus/RunParameters.xml', + "$runfolder_path/RunParameters.xml"; + +subtest 'a new run in incoming' => sub { + plan tests => 15; + + my $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $size_hash = {}; + my $done; + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok (!$done, 'correct return value'); + ok (defined $monitor->tracking_run(), 'run row is cached'); + my $tracking_run = $monitor->tracking_run(); + is ($tracking_run->id_run, $id_run, 'correct db record is cached'); + is ($tracking_run->folder_name(), $runfolder_name, + 'tracking database - run folder name is set'); + is ($tracking_run->folder_path_glob(), "$dir/*/", + 'tracking database - run folder glob is set'); + is ($tracking_run->actual_cycle_count(), 0, 'cycle count is zero'); + is ($tracking_run->current_run_status_description(), 'run pending', + 'the run is still pending'); + is ($tracking_run->flowcell_id(), '225TGJLT3', + 'flowcell barcode is recorded'); + ok ($tracking_run->is_tag_set('staging'), 'staging tag is set'); + ok ($tracking_run->is_tag_set('fc_slotB'), 'instrument side B is set'); + ok ($tracking_run->is_tag_set('paired_read'), 'run is tagged as paired'); + ok ($tracking_run->is_tag_set('multiplex'), 'run is tagged as multiplex'); + ok (exists $size_hash->{$runfolder_path}, 'runfolder size is cached'); + is ($size_hash->{$runfolder_path}, 0, 'runfolder size is set to zero'); +}; + +subtest 'run in progress' => sub { + plan tests => 10; + + # Now the run is half way through to completion. + for my $i ((1 .. 8)) { + for my $j ((1 .. 4)) { + make_path("$basecalls_path/L00${i}/C${j}.1"); + } + } + my $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $size_hash = {$runfolder_path => 0}; + my $done; + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok (!$done, 'correct return value'); + is ($monitor->tracking_run->actual_cycle_count(), 4, 'cycle count is 4'); + is ($monitor->tracking_run->current_run_status_description(), 'run in progress', + 'the run is in progress'); + is ($size_hash->{$runfolder_path}, 0, 'runfolder size is zero'); + + # Now the run is close to completion. + for my $i ((1 .. 8)) { + for my $j ((5 .. 8)) { + make_path("$basecalls_path/L00${i}/C${j}.1"); + } + } + $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok (!$done, 'correct return value'); + is ($monitor->tracking_run->actual_cycle_count(), 8, 'cycle count is 8'); + is ($monitor->tracking_run->current_run_status_description(), 'run in progress', + 'the run is in progress'); + is ($size_hash->{$runfolder_path}, 0, 'runfolder size is zero'); +}; + +subtest 'run is completed' => sub { + plan tests => 5; + + for my $f (qw(RTAComplete.txt CopyComplete.txt)) { + `touch $runfolder_path/$f`; + } + + my $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $size_hash = {$runfolder_path => 0}; + my $done; + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok (!$done, 'correct return value'); + is ($monitor->tracking_run->actual_cycle_count(), 8, 'cycle count is 8'); + is ($monitor->tracking_run->current_run_status_description(), 'run complete', + 'the run has completed'); + is ($size_hash->{$runfolder_path}, 0, 'runfolder size is zero'); +}; + +subtest 'run is mirrored' => sub { + plan tests => 10; + + for my $i ((1 .. 8)) { + for my $j ((1 .. 8)) { + for my $s ((1 .. 2)) { + `touch $basecalls_path/L00${i}/C${j}.1/L00${i}_${s}.cbcl`; + } + } + } + my $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $size_hash = {$runfolder_path => 0}; + my $done; + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok (!$done, 'correct return value'); + my $size = $size_hash->{$runfolder_path}; + ok ($size > 0, 'runfolder size is not zero'); + is ($monitor->tracking_run->current_run_status_description(), 'run complete', + 'the run is still marked as completed'); + + $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok ($done, 'correct return value'); + is ($size_hash->{$runfolder_path}, $size, 'runfolder size does not change'); + is ($monitor->tracking_run->current_run_status_description(), 'analysis pending', + 'the run is marked as mirrored and automatically moved to pending analysis'); + ok (!-e $runfolder_path, 'the old run folder path is invalid'); + $runfolder_path = join q[/], $adir, $runfolder_name; + ok (-e $runfolder_path, q[the folder has been moved to 'analysis']); +}; + +subtest q[move to 'outgoing'] => sub { + plan tests => 10; + + # Run is now in the 'analysis' directory' + $run->update_run_status('secondary analysis in progress'); + my $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $done; + lives_ok { $done = $monitor->update_run_from_path({}) } 'run the monitor'; + ok (!$done, 'correct return value'); + ok (-e $runfolder_path, q[run folder is still in 'analysis']); + + $run->update_run_status('qc complete'); + $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $inhibit_folder_move = 1; + lives_ok { $done = $monitor->update_run_from_path({}, $inhibit_folder_move ) } + 'run the monitor'; + ok (!$done, 'correct return value'); + ok (-e $runfolder_path, q[run folder is still in 'analysis']); + + lives_ok { $done = $monitor->update_run_from_path({}) } 'run the monitor'; + ok (!$done, 'correct return value'); + ok (!-e $runfolder_path, 'the old run folder path is invalid'); + $runfolder_path = join q[/], $odir, $runfolder_name; + ok (-e $runfolder_path, q[the folder has been moved to 'outgoing']); +}; + +subtest q[wait for DRAGEN analysis to finish] => sub { + plan tests => 13; + + # Change the run status. + sleep 1; # Ensure a different timestamp for the new status. + $run->update_run_status('run complete'); + + my $new_path = join q[/], $idir, $runfolder_name; + `mv $runfolder_path $new_path`; # Move the run folder back to 'incoming'. + $runfolder_path = $new_path; + # Copy the file with the DRAGEN analysis section. + copy('t/data/run_params/RunParameters.novaseqx.onboard.xml', + "$runfolder_path/RunParameters.xml"); + my $dpath = "$runfolder_path/Analysis/1"; + make_path($dpath); # Create DRAGEN analysis directory. + + my $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + my $size_hash = {$runfolder_path => 0}; + my $done; + lives_ok { $done = $monitor->update_run_from_path($size_hash) } + 'run the monitor'; + ok (!$done, 'correct return value'); + ok ($monitor->onboard_analysis_planned(), 'onboard analysis is planned'); + ok (!$monitor->is_onboard_analysis_output_copied(), + 'onboard analysis data is not copied across yet'); + ok (-e $runfolder_path, q[run folder is in 'incoming']); + my $size = $size_hash->{$runfolder_path}; + + $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + ok (!$done, 'correct return value'); + ok (-e $runfolder_path, q[run folder is still in 'incoming']); + ok ($size_hash->{$runfolder_path} == $size, 'the run folder size is stable'); + ok (!$monitor->is_onboard_analysis_output_copied(), + 'onboard analysis data is not copied across yet'); + + # Mark DRAGEN analysis as copied across. + open my $fh, q[>], "$dpath/CopyComplete.txt" or die 'Cannot open the file'; + print $fh 'Mark DRAGEN analysis as copied' or die 'Cannot write'; + close $fh or die 'Cannot close the filehandle'; + + $monitor = Monitor::RunFolder::Staging->new( + runfolder_path => $runfolder_path, + npg_tracking_schema => $schema + ); + lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; + # Sometimes the runfolder size comes out differently at this point, + # and and extra round is needed. + if (!$done) { + $monitor->update_run_from_path($size_hash); + } + ok (!-e $runfolder_path, 'the old run folder path is invalid'); + $runfolder_path = join q[/], $adir, $runfolder_name; + ok (-e $runfolder_path, q[the folder has been moved to 'analysis']); +}; + +1; + + + diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t new file mode 100644 index 00000000..3e0c5e70 --- /dev/null +++ b/t/47-npg_samplesheet_auto.t @@ -0,0 +1,50 @@ +use strict; +use warnings; +use Test::More tests => 9; +use Test::Exception; +use File::Temp qw/ tempdir /; +use Moose::Meta::Class; + +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 $sm; + lives_ok { $sm = npg::samplesheet::auto->new( + npg_tracking_schema => $schema, + mlwh_schema => $schema_wh) } 'miseq monitor object'; + isa_ok($sm, 'npg::samplesheet::auto'); +} + +{ + is(npg::samplesheet::auto::_id_run_from_samplesheet( + 't/data/samplesheet/miseq_default.csv'), 10262, + 'id run retrieved from a samplesheet'); + lives_and { is npg::samplesheet::auto::_id_run_from_samplesheet('some_file'), undef} + 'undef reftuned for a non-exisitng samplesheet'; +} + +{ + my $dir = tempdir(UNLINK => 1); + my $file = join q[/], $dir, 'myfile'; + `touch $file`; + npg::samplesheet::auto::_move_samplesheet($file); + ok(!-e $file, 'original file does not exist'); + ok(-e $file.'_invalid', 'file has been moved'); + + my $sdir = join q[/], $dir, 'samplesheet'; + mkdir $sdir; + mkdir $sdir . '_old'; + $file = join q[/], $sdir, 'myfile'; + `touch $file`; + my $new_file = join q[/], $sdir . '_old', 'myfile_invalid'; + npg::samplesheet::auto::_move_samplesheet($file); + ok(!-e $file, 'original file does not exist'); + ok(-e $new_file, 'moved file is in samplesheet_old directory'); +} + +1; diff --git a/t/47-npg_samplesheet_novaseq_xseries.t b/t/47-npg_samplesheet_novaseq_xseries.t index e122b820..15f5cedb 100644 --- a/t/47-npg_samplesheet_novaseq_xseries.t +++ b/t/47-npg_samplesheet_novaseq_xseries.t @@ -12,7 +12,7 @@ use_ok('npg::samplesheet::novaseq_xseries'); my $class = Moose::Meta::Class->create_anon_class(roles=>[qw/npg_testing::db/]); my $schema_tracking = $class->new_object({})->create_test_db( - q[npg_tracking::Schema], q[t/data/dbic_fixtures] + q[npg_tracking::Schema], q[t/data/dbic_fixtures] ); my $schema_wh = $class->new_object({})->create_test_db( @@ -22,7 +22,7 @@ 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 => 13; + plan tests => 14; my $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, @@ -51,21 +51,21 @@ subtest 'create the generator object, test simple attributes' => sub { like($g->run_name, qr/\Assbatch97071_[\w]+\Z/, 'run name when id_run is not given'); like($g->file_name, qr/\A${date}_ssbatch97071_[\w]+\.csv\Z/, - 'samplesheet file name when id_run is not given'); - - $g = npg::samplesheet::novaseq_xseries->new( - npg_tracking_schema => $schema_tracking, - mlwh_schema => $schema_wh, - id_run => 47446, - batch_id => 97071, - ); - is($g->run_name, '47446', 'run name is run ID when the latter is known'); + 'samplesheet file name when id_run is not given'); + my $run_row = $schema_tracking->resultset('Run')->create({ id_run => 47446, id_instrument_format => 12, id_instrument => 69, team => 'A' }); + + $g = npg::samplesheet::novaseq_xseries->new( + npg_tracking_schema => $schema_tracking, + mlwh_schema => $schema_wh, + id_run => 47446, + batch_id => 97071, + ); throws_ok { $g->file_name } qr/Slot is not set for run 47446/, 'error when the slot is unknown'; @@ -78,13 +78,15 @@ subtest 'create the generator object, test simple attributes' => sub { id_run => 47446, batch_id => 97071, ); - is ($g->file_name, "${date}_NVX1_47446_${slot}_ssbatch97071.csv", + is ($g->file_name, "${date}_47446_NVX1_${slot}_ssbatch97071.csv", 'correct file name is generated'); + is($g->run_name, "47446_NVX1_${slot}", + 'run name is constructed from run ID when possible'); if ($slot eq 'A') { $run_row->unset_tag($tag); } } - + $g = npg::samplesheet::novaseq_xseries->new( npg_tracking_schema => $schema_tracking, mlwh_schema => $schema_wh, @@ -100,7 +102,7 @@ subtest 'create the generator object, test simple attributes' => sub { mlwh_schema => $schema_wh, id_run => 47446, ); - is ($g->file_name, "${date}_NVX1_47446_B_ssbatch99888.csv", + is ($g->file_name, "${date}_47446_NVX1_B_ssbatch99888.csv", 'correct file name is generated'); $run_row->update({id_instrument_format => 10, id_instrument => 68}); @@ -111,7 +113,7 @@ subtest 'create the generator object, test simple attributes' => sub { ); throws_ok { $g->file_name } qr/Instrument model is not NovaSeq X Series/, - 'error when the run is registered on the wrong instrument model'; + 'error when the run is registered on the wrong instrument model'; }; 1; diff --git a/t/60-illumina-run-long_info.t b/t/60-illumina-run-long_info.t index e92058a1..ab44defe 100644 --- a/t/60-illumina-run-long_info.t +++ b/t/60-illumina-run-long_info.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 67; +use Test::More tests => 68; use Test::Exception; use Test::Deep; use File::Temp qw(tempdir); @@ -29,7 +29,7 @@ package main; my $basedir = tempdir( CLEANUP => 1 ); subtest 'retrieving information from runParameters.xml' => sub { - plan tests => 153; + plan tests => 167; my $rf = join q[/], $basedir, 'runfolder'; mkdir $rf; @@ -118,10 +118,31 @@ subtest 'retrieving information from runParameters.xml' => sub { ok (!$li->uses_patterned_flowcell, 'not patterned flowcell'); } + ok (!$li->onboard_analysis_planned(), 'onboard analysis is not planned'); + unlink $name; } }; +subtest 'detecting onboard analysis' => sub { + plan tests => 1; + + my $rf = join q[/], $basedir, 'runfolder_onboard'; + mkdir $rf; + copy('t/data/run_params/RunParameters.novaseqx.onboard.xml', + "$rf/RunParameters.xml"); + + my $class = Moose::Meta::Class->create_anon_class( + methods => {"runfolder_path" => sub {$rf}}, + roles => [qw/npg_tracking::illumina::run::long_info/] + ); + my $li = $class->new_object(); + ok ($li->onboard_analysis_planned(), 'onboard analysis is planned'); + + my $o = $li->onboard_analysis_planned(); + diag $o; +}; + subtest 'getting i5opposite for run' => sub { plan tests => 19; diff --git a/t/60-illumina-run-short_info.t b/t/60-illumina-run-short_info.t index 4fadfd48..9777e889 100644 --- a/t/60-illumina-run-short_info.t +++ b/t/60-illumina-run-short_info.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 45; +use Test::More tests => 46; use Test::Exception; use File::Temp qw/ tempdir /; use Moose::Meta::Class; @@ -30,7 +30,7 @@ sub _build_run_folder { my $path = $self->_short_path(); return first {$_ ne q()} reverse splitdir($path); - + } @@ -39,7 +39,7 @@ has q{_short_path} => ( isa => q{Str}, is => q{ro}, lazy_build => sub _build__short_path { my ($self) = @_; my @dir = $self->has_run_folder() ? glob $self->_folder_path_glob_pattern() . $self->run_folder() - : $self->has_id_run() ? glob $self->_folder_path_glob_pattern() . q(*_{r,}) . $self->id_run() . q{*} + : $self->has_id_run() ? glob $self->_folder_path_glob_pattern() . q(*_{r,}) . $self->id_run() . q{*} : $self->has_name() ? glob $self->_folder_path_glob_pattern() . q{*} . $self->name() : croak q{No run_folder, name or id_run provided} ; @@ -71,6 +71,12 @@ sub _folder_path_glob_pattern { } +package test::nvx_short_info; +use Moose; +with 'npg_tracking::illumina::run::short_info'; + +has experiment_name => (is => 'rw'); + package main; sub create_staging { @@ -187,7 +193,7 @@ my $run_folder = q{123456_IL2_1234}; }); is($short_info->short_reference(), $id_run, q{HS short_reference returns id_run}); is($short_info->name(),q{HS2_1234}, q{HS name worked out correctly}); - is($short_info->short_reference(), q{123456_HS2_1234_B_205NNABXX}, q{HS short_reference returns run_folder}); + is($short_info->short_reference(), q{123456_HS2_1234_B_205NNABXX}, q{HS short_reference returns run_folder}); } #### test where name is give in the constructor @@ -243,7 +249,7 @@ my $run_folder = q{123456_IL2_1234}; my $name; my $flowcell_id; - lives_ok { + lives_ok { $name = $short_info->name(); $flowcell_id= $short_info->flowcell_id(); } q{MiSeq runfolder - kit id in place of flowcell}; @@ -265,4 +271,28 @@ subtest 'process run_folder when no id_run present' => sub { } qr[Unable to identify id_run], q[Throws when it obtain id_run]; }; +subtest 'Test id_run extraction from within experiment_name' => sub { + plan tests => 7; + my $short_info = test::nvx_short_info->new(experiment_name => '45678_NVX1_A', run_folder => 'not_a_folder'); + is($short_info->id_run, '45678', 'id_run parsed from experiment name'); + + $short_info = test::nvx_short_info->new(experiment_name => ' 45678_NVX1_A ', run_folder => 'not_a_folder'); + is($short_info->id_run, '45678', 'id_run parsed from loosely formatted experiment name'); + + $short_info = test::nvx_short_info->new(experiment_name => '45678_NVX1_A ', run_folder => 'not_a_folder'); + is($short_info->id_run, '45678', 'id_run parsed from experiment name with postfix spaces'); + + $short_info = test::nvx_short_info->new(experiment_name => ' 45678_NVX1_A', run_folder => 'not_a_folder'); + is($short_info->id_run, '45678', 'id_run parsed from experiment name with prefixed spaces'); + + $short_info = test::nvx_short_info->new(experiment_name => '45678', run_folder => 'not_a_folder'); + is($short_info->id_run, '45678', 'Bare id_run as experiment name is fine'); + + $short_info = test::nvx_short_info->new(experiment_name => 'NovaSeqX_WHGS_TruSeqPF_NA12878', run_folder => 'not_a_folder'); + throws_ok { $short_info->id_run } qr{Unable to identify id_run with data provided}, 'Custom run name cannot be parsed'; + + $short_info = test::nvx_short_info->new(id_run => '45678', experiment_name => '56789_NVX1_A', run_folder => 'not_a_folder'); + is($short_info->id_run, '45678', 'Set id_run wins over experiment_name'); +}; + 1; diff --git a/t/data/dbic_fixtures/100-InstrumentFormat.yml b/t/data/dbic_fixtures/100-InstrumentFormat.yml index bd97d3cb..12010813 100644 --- a/t/data/dbic_fixtures/100-InstrumentFormat.yml +++ b/t/data/dbic_fixtures/100-InstrumentFormat.yml @@ -49,3 +49,9 @@ iscurrent: 1 default_tiles: 0 default_columns: 0 +- id_instrument_format: 14 + id_manufacturer: 10 + model: NovaSeqXPlus + iscurrent: 1 + default_tiles: 0 + default_columns: 0 diff --git a/t/data/dbic_fixtures/200-Instrument.yml b/t/data/dbic_fixtures/200-Instrument.yml index 92ce84a4..28b4927c 100644 --- a/t/data/dbic_fixtures/200-Instrument.yml +++ b/t/data/dbic_fixtures/200-Instrument.yml @@ -126,5 +126,18 @@ staging_dir: latest_contact: percent_complete: - lab: Ogilvie + lab: Ogilvie +- id_instrument: 70 + name: NVX2 + id_instrument_format: 14 + external_name: 'LH00210' + serial: '' + iscurrent: 1 + ipaddr: + instrument_comp: + mirroring_host: + staging_dir: + latest_contact: + percent_complete: + lab: Ogilvie diff --git a/t/data/dbic_fixtures/300-Run.yml b/t/data/dbic_fixtures/300-Run.yml index 36bbfc2f..eb0798bd 100644 --- a/t/data/dbic_fixtures/300-Run.yml +++ b/t/data/dbic_fixtures/300-Run.yml @@ -9,7 +9,7 @@ team: 'RAD' is_paired: 0 priority: 1 - flowcell_id: + flowcell_id: - actual_cycle_count: 64 batch_id: 4861 expected_cycle_count: 64 diff --git a/t/data/fixtures_lims_transcriptome/000-Sample.yml b/t/data/fixtures_lims_transcriptome/000-Sample.yml new file mode 100644 index 00000000..b78e7998 --- /dev/null +++ b/t/data/fixtures_lims_transcriptome/000-Sample.yml @@ -0,0 +1,1703 @@ +--- +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: ~ + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-08-06 14:24:41 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1255141 + id_sample_tmp: 1237247 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:48:50 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: phiX_for_spiked_buffers + organism: ~ + organism_part: ~ + phenotype: ~ + public_name: ~ + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:28:54 + reference_genome: PhiX (Sanger-SNPs) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 10847 + time_point: ~ + treatment: ~ + uuid_sample_lims: d3a59c4c-c037-11e0-834c-00144f01a414 +- accession_number: ~ + age: 14 weeks + cell_type: N/A + cohort: ~ + common_name: Mus musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-06 09:30:37 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: RNA from MOE of the brain of S-cross + developmental_stage: Adult + disease: N/A + disease_state: N/A + dna_source: Brain + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: CAST/EiJ + gc_content: Neutral + gender: Female + genotype: F1 hybred + geographical_region: ~ + growth_condition: Normal + id_lims: SQSCP + id_sample_lims: 1807467 + id_sample_tmp: 1785733 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:39:58 + marked_as_consent_withdrawn_by: ~ + mother: C57BL/6J + name: ZSL_S1_MOE + organism: Mouse + organism_part: Brain + phenotype: N/A + public_name: mBLpCAST-1-MOE + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:46:46 + reference_genome: Mus_musculus (GRCm38) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: F1 hybred + subject: N/A + supplier_name: ~ + taxon_id: 10090 + time_point: N/A + treatment: N/A + uuid_sample_lims: 333275f0-76b5-11e3-9714-68b59976a382 +- accession_number: ~ + age: 14 weeks + cell_type: N/A + cohort: ~ + common_name: Mus musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-06 09:30:37 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: RNA from MOE of the brain of S-cross + developmental_stage: Adult + disease: N/A + disease_state: N/A + dna_source: Brain + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: CAST/EiJ + gc_content: Neutral + gender: Female + genotype: F1 hybred + geographical_region: ~ + growth_condition: Normal + id_lims: SQSCP + id_sample_lims: 1807468 + id_sample_tmp: 1785734 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:39:58 + marked_as_consent_withdrawn_by: ~ + mother: C57BL/6J + name: ZSL_S2_MOE + organism: Mouse + organism_part: Brain + phenotype: N/A + public_name: mBLpCAST-2-MOE + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:46:46 + reference_genome: Mus_musculus (GRCm38) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: F1 hybred + subject: N/A + supplier_name: ~ + taxon_id: 10090 + time_point: N/A + treatment: N/A + uuid_sample_lims: 3366f370-76b5-11e3-9714-68b59976a382 +- accession_number: ~ + age: 14 weeks + cell_type: N/A + cohort: ~ + common_name: Mus musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-06 09:30:37 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: RNA from MOE of the brain of S-cross + developmental_stage: Adult + disease: N/A + disease_state: N/A + dna_source: Brain + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: CAST/EiJ + gc_content: Neutral + gender: Female + genotype: F1 hybred + geographical_region: ~ + growth_condition: Normal + id_lims: SQSCP + id_sample_lims: 1807469 + id_sample_tmp: 1785735 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:39:58 + marked_as_consent_withdrawn_by: ~ + mother: C57BL/6J + name: ZSL_S3_MOE + organism: Mouse + organism_part: Brain + phenotype: N/A + public_name: mBLpCAST-3-MOE + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:46:46 + reference_genome: Mus_musculus (GRCm38) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: F1 hybred + subject: N/A + supplier_name: ~ + taxon_id: 10090 + time_point: N/A + treatment: N/A + uuid_sample_lims: 3386b070-76b5-11e3-9714-68b59976a382 +- accession_number: ~ + age: 14 weeks + cell_type: N/A + cohort: ~ + common_name: Mus musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-06 09:30:37 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: RNA from MOE of the brain of S-cross + developmental_stage: Adult + disease: N/A + disease_state: N/A + dna_source: Brain + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: CAST/EiJ + gc_content: Neutral + gender: Female + genotype: F1 hybred + geographical_region: ~ + growth_condition: Normal + id_lims: SQSCP + id_sample_lims: 1807470 + id_sample_tmp: 1785736 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:39:58 + marked_as_consent_withdrawn_by: ~ + mother: C57BL/6J + name: ZSL_S4_MOE + organism: Mouse + organism_part: Brain + phenotype: N/A + public_name: mBLpCAST-4-MOE + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:46:46 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time_point: N/A + treatment: N/A + uuid_sample_lims: 34a518c0-76b5-11e3-9714-68b59976a382 +- accession_number: ~ + age: 14 weeks + cell_type: N/A + cohort: ~ + common_name: Mus musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-06 09:30:39 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: RNA from OB of the brain of M-cross + developmental_stage: Adult + disease: N/A + disease_state: N/A + dna_source: Brain + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: C57BL/6J + gc_content: Neutral + gender: Female + genotype: F1 hybred + geographical_region: ~ + growth_condition: Normal + id_lims: SQSCP + id_sample_lims: 1807485 + id_sample_tmp: 1785751 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:39:58 + marked_as_consent_withdrawn_by: ~ + mother: CAST/EiJ + name: ZSL_M4_BULB + organism: Mouse + organism_part: Brain + phenotype: N/A + public_name: mCASTpBL-4-OB + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:46:47 + reference_genome: Mus_musculus (GRCm38) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: F1 hybred + subject: N/A + supplier_name: ~ + taxon_id: 10090 + time_point: N/A + treatment: N/A + uuid_sample_lims: 34b915f0-76b5-11e3-9714-68b59976a382 +- accession_number: ~ + age: 14 weeks + cell_type: N/A + cohort: ~ + common_name: Mus musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-06 09:30:39 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: RNA from OB of the brain of M-cross + developmental_stage: Adult + disease: N/A + disease_state: N/A + dna_source: Brain + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: C57BL/6J + gc_content: Neutral + gender: Female + genotype: F1 hybred + geographical_region: ~ + growth_condition: Normal + id_lims: SQSCP + id_sample_lims: 1807486 + id_sample_tmp: 1785752 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:39:58 + marked_as_consent_withdrawn_by: ~ + mother: CAST/EiJ + name: ZSL_M5_BULB + organism: Mouse + organism_part: Brain + phenotype: N/A + public_name: mCASTpBL-5-OB + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:46:47 + reference_genome: Mus_musculus (GRCm38) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: F1 hybred + subject: N/A + supplier_name: ~ + taxon_id: 10090 + time_point: N/A + treatment: N/A + uuid_sample_lims: 34cbdaa0-76b5-11e3-9714-68b59976a382 +- accession_number: ~ + age: N/A + cell_type: iPS-derived macrophage + cohort: ~ + common_name: Homo sapiens + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-28 11:23:55 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: Total RNA from iPS-derived macrophages using mirVana + developmental_stage: N/A + disease: N/A + disease_state: N/A + dna_source: Genomic + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: Not Applicable + genotype: N/A + geographical_region: ~ + growth_condition: N/A + id_lims: SQSCP + id_sample_lims: 1830658 + id_sample_tmp: 1808338 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:41:26 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: abc + organism: Human + organism_part: N/A + phenotype: Normal + public_name: abc + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:49:44 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: N/A + treatment: control + uuid_sample_lims: ac43efe0-880e-11e3-a7f3-68b59976a382 +- accession_number: ~ + age: N/A + cell_type: iPS-derived macrophage + cohort: ~ + common_name: Homo sapiens + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-28 11:23:55 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: Total RNA from iPS-derived macrophages using mirVana + developmental_stage: N/A + disease: N/A + disease_state: N/A + dna_source: Genomic + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: Not Applicable + genotype: N/A + geographical_region: ~ + growth_condition: N/A + id_lims: SQSCP + id_sample_lims: 1830659 + id_sample_tmp: 1808339 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:41:26 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: abc + organism: Human + organism_part: N/A + phenotype: Normal + public_name: abc + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:49:44 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: N/A + treatment: LPS + uuid_sample_lims: ac816e10-880e-11e3-a7f3-68b59976a382 +- accession_number: ~ + age: N/A + cell_type: iPS-derived macrophage + cohort: ~ + common_name: Homo sapiens + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-28 11:23:55 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: Total RNA from iPS-derived macrophages using mirVana + developmental_stage: N/A + disease: N/A + disease_state: N/A + dna_source: Genomic + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: Not Applicable + genotype: N/A + geographical_region: ~ + growth_condition: N/A + id_lims: SQSCP + id_sample_lims: 1830660 + id_sample_tmp: 1808340 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:41:26 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: abc + organism: Human + organism_part: N/A + phenotype: Normal + public_name: abc + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:49:44 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: N/A + treatment: control + uuid_sample_lims: ac9bfaf0-880e-11e3-a7f3-68b59976a382 +- accession_number: ~ + age: N/A + cell_type: iPS-derived macrophage + cohort: ~ + common_name: Homo sapiens + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-01-28 11:23:55 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: Total RNA from iPS-derived macrophages using mirVana + developmental_stage: N/A + disease: N/A + disease_state: N/A + dna_source: Genomic + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: Not Applicable + genotype: N/A + geographical_region: ~ + growth_condition: N/A + id_lims: SQSCP + id_sample_lims: 1830661 + id_sample_tmp: 1808341 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:41:26 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: abc + organism: Human + organism_part: N/A + phenotype: Normal + public_name: abc + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:49:44 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: N/A + treatment: LPS + uuid_sample_lims: acb6aee0-880e-11e3-a7f3-68b59976a382 +- accession_number: ~ + age: N/A + cell_type: iPS-derived macrophage + cohort: ~ + common_name: Homo sapiens + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-02-05 12:29:16 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: Total RNA from iPS-derived macrophages using mirVana + developmental_stage: N/A + disease: N/A + disease_state: N/A + dna_source: Genomic + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: Not Applicable + genotype: N/A + geographical_region: ~ + growth_condition: N/A + id_lims: SQSCP + id_sample_lims: 1846288 + id_sample_tmp: 1823966 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:42:25 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: abc + organism: Human + organism_part: N/A + phenotype: Normal + public_name: abc + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:51:39 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: N/A + treatment: control + uuid_sample_lims: 21000c30-8e61-11e3-b3b8-68b59976a382 +- accession_number: ~ + age: N/A + cell_type: iPS-derived macrophage + cohort: ~ + common_name: Homo sapiens + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2014-02-05 12:29:16 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: Total RNA from iPS-derived macrophages using mirVana + developmental_stage: N/A + disease: N/A + disease_state: N/A + dna_source: Genomic + donor_id: ~ + dose: N/A + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: Not Applicable + genotype: N/A + geographical_region: ~ + growth_condition: N/A + id_lims: SQSCP + id_sample_lims: 1846289 + id_sample_tmp: 1823967 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:42:25 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: abc + organism: Human + organism_part: N/A + phenotype: Normal + public_name: abc + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 21:51:39 + reference_genome: Homo_sapiens (1000Genomes_hs37d5) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: N/A + treatment: LPS + uuid_sample_lims: 2119fcd0-8e61-11e3-b3b8-68b59976a382 + diff --git a/t/data/fixtures_lims_transcriptome/000-Study.yml b/t/data/fixtures_lims_transcriptome/000-Study.yml new file mode 100644 index 00000000..fa4c0d0c --- /dev/null +++ b/t/data/fixtures_lims_transcriptome/000-Study.yml @@ -0,0 +1,122 @@ +--- +- abbreviation: 198STDY + abstract: ~ + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2008-11-13 13:27:48 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genotyping or cytogenetics + data_release_strategy: open + data_release_timing: standard + deleted_at: ~ + description: None + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: None + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 198 + id_study_tmp: 177 + last_updated: 2021-10-15 08:54:34 + name: Illumina Controls + prelim_id: ~ + recorded_at: 2021-10-15 08:54:35 + reference_genome: ' ' + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: ~ + study_type: Resequencing + study_visibility: Hold + uuid_study_lims: 2aa1cd2e-a557-11df-8092-00144f01a414 +- abbreviation: 2899STDY + abstract: ~ + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2014-01-06 09:24:16 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: transcriptomics + data_release_strategy: open + data_release_timing: standard + deleted_at: ~ + description: ~ + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: ~ + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 2899 + id_study_tmp: 2866 + last_updated: 2021-10-15 08:55:26 + name: Parent-of-origin allelic expression bias in mouse olfaction system + prelim_id: ~ + recorded_at: 2021-10-15 08:55:40 + reference_genome: Mus_musculus (GRCm38) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Detecting parent-of-origin allelic expression bias in mouse olfaction system + study_type: Transcriptome Analysis + study_visibility: Hold + uuid_study_lims: 5060f850-76b4-11e3-9e87-68b59976a382 +- abbreviation: macrophage_miRNA + abstract: ~ + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 1 + contaminated_human_dna: 0 + created: 2014-01-14 10:49:48 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: transcriptomics + data_release_strategy: managed + data_release_timing: standard + deleted_at: ~ + description: ~ + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: 1 + faculty_sponsor: ~ + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 2910 + id_study_tmp: 2877 + last_updated: 2021-10-15 08:55:27 + name: 'I1548 - miRNA expression in response to LPS stimulus in macrophages' + prelim_id: ~ + recorded_at: 2021-10-15 08:55:40 + reference_genome: ~ + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: miRNA expression in response to LPS stimulus in macrophages + study_type: Transcriptome Analysis + study_visibility: Hold + uuid_study_lims: 9699b400-7d09-11e3-b3de-68b59976a382 + diff --git a/t/data/fixtures_lims_transcriptome/100-IseqFlowcell.yml b/t/data/fixtures_lims_transcriptome/100-IseqFlowcell.yml new file mode 100644 index 00000000..38a8c845 --- /dev/null +++ b/t/data/fixtures_lims_transcriptome/100-IseqFlowcell.yml @@ -0,0 +1,1163 @@ +--- +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889563 + id_library_lims: NT356545P + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785733 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155523 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 1 + tag_index: 1 + tag_sequence: ATCACG + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889564 + id_library_lims: NT356546Q + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785734 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155524 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 2 + tag_index: 2 + tag_sequence: CGATGT + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889565 + id_library_lims: NT356547R + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785735 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155525 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 3 + tag_index: 3 + tag_sequence: TTAGGC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889566 + id_library_lims: NT356548S + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785736 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155526 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 4 + tag_index: 4 + tag_sequence: TGACCA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889567 + id_library_lims: NT356549T + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785737 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155527 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 5 + tag_index: 5 + tag_sequence: ACAGTG + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889568 + id_library_lims: NT356550M + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785738 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155528 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 6 + tag_index: 6 + tag_sequence: GCCAAT + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889569 + id_library_lims: NT356551N + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785739 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155529 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 7 + tag_index: 7 + tag_sequence: CAGATC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889570 + id_library_lims: NT356552O + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785740 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155530 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 8 + tag_index: 8 + tag_sequence: ACTTGA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889571 + id_library_lims: NT356553P + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785741 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155531 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 9 + tag_index: 9 + tag_sequence: GATCAG + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889572 + id_library_lims: NT356554Q + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785742 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155532 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 10 + tag_index: 10 + tag_sequence: TAGCTT + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889573 + id_library_lims: NT356555R + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785743 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155533 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 11 + tag_index: 11 + tag_sequence: GGCTAC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889574 + id_library_lims: NT356556S + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785744 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155534 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 12 + tag_index: 12 + tag_sequence: CTTGTA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889575 + id_library_lims: NT356557T + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785745 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155535 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 13 + tag_index: 13 + tag_sequence: AGTCAA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889576 + id_library_lims: NT356558U + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785746 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155536 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 14 + tag_index: 14 + tag_sequence: AGTTCC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889577 + id_library_lims: NT356559V + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785747 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155537 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 15 + tag_index: 15 + tag_sequence: ATGTCA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889578 + id_library_lims: NT356560O + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785748 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155538 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 16 + tag_index: 16 + tag_sequence: CCGTCC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889579 + id_library_lims: NT356561P + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785749 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155539 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:22 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 17 + tag_index: 17 + tag_sequence: GTCCGC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889580 + id_library_lims: NT356562Q + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785750 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155540 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:22 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 18 + tag_index: 18 + tag_sequence: GTGAAA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889581 + id_library_lims: NT356563R + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785751 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155541 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:22 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 19 + tag_index: 19 + tag_sequence: GTGGCC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9327018 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889582 + id_library_lims: NT356564S + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1785752 + id_study_tmp: 2866 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 9155542 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Illumina cDNA protocol + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:22 + requested_insert_size_from: 200 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 20 + tag_index: 20 + tag_sequence: GTTTCG + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 9327018 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2N5GACXX + forward_read_length: 100 + id_flowcell_lims: 25539 + id_iseq_flowcell_tmp: 2889562 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT357120V + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:31:19 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:31:21 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9416272 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 25 + id_flowcell_lims: 25715 + id_iseq_flowcell_tmp: 3046395 + id_library_lims: NT364634M + id_lims: SQSCP + id_pool_lims: NT365034V + id_sample_tmp: 1808338 + id_study_tmp: 2877 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2015-06-08 15:20:09 + legacy_library_id: 9376962 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Small RNA + position: 1 + primer_panel: ~ + priority: 0 + purpose: ~ + recorded_at: 2015-06-08 15:20:21 + requested_insert_size_from: 17 + requested_insert_size_to: 30 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 1 + tag_index: 1 + tag_sequence: ATCACG + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9416272 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 25 + id_flowcell_lims: 25715 + id_iseq_flowcell_tmp: 3046396 + id_library_lims: NT364635N + id_lims: SQSCP + id_pool_lims: NT365034V + id_sample_tmp: 1808339 + id_study_tmp: 2877 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2015-06-08 15:20:09 + legacy_library_id: 9376963 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Small RNA + position: 1 + primer_panel: ~ + priority: 0 + purpose: ~ + recorded_at: 2015-06-08 15:20:21 + requested_insert_size_from: 17 + requested_insert_size_to: 30 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 2 + tag_index: 2 + tag_sequence: CGATGT + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9416272 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 25 + id_flowcell_lims: 25715 + id_iseq_flowcell_tmp: 3046397 + id_library_lims: NT364636O + id_lims: SQSCP + id_pool_lims: NT365034V + id_sample_tmp: 1808340 + id_study_tmp: 2877 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2015-06-08 15:20:09 + legacy_library_id: 9376964 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Small RNA + position: 1 + primer_panel: ~ + priority: 0 + purpose: ~ + recorded_at: 2015-06-08 15:20:21 + requested_insert_size_from: 17 + requested_insert_size_to: 30 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 3 + tag_index: 3 + tag_sequence: TTAGGC + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9416272 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 25 + id_flowcell_lims: 25715 + id_iseq_flowcell_tmp: 3046398 + id_library_lims: NT364637P + id_lims: SQSCP + id_pool_lims: NT365034V + id_sample_tmp: 1808341 + id_study_tmp: 2877 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2015-06-08 15:20:09 + legacy_library_id: 9376965 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Small RNA + position: 1 + primer_panel: ~ + priority: 0 + purpose: ~ + recorded_at: 2015-06-08 15:20:21 + requested_insert_size_from: 17 + requested_insert_size_to: 30 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 4 + tag_index: 4 + tag_sequence: TGACCA + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0755 + entity_id_lims: 9416272 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: ~ + forward_read_length: 25 + id_flowcell_lims: 25715 + id_iseq_flowcell_tmp: 3046399 + id_library_lims: NT364638Q + id_lims: SQSCP + id_pool_lims: NT365034V + id_sample_tmp: 1823966 + id_study_tmp: 2877 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2015-06-08 15:20:09 + legacy_library_id: 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2015-06-08 15:20:09 + legacy_library_id: 9376967 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Small RNA + position: 1 + primer_panel: ~ + priority: 0 + purpose: ~ + recorded_at: 2015-06-08 15:20:21 + requested_insert_size_from: 17 + requested_insert_size_to: 30 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 6 + tag_index: 6 + tag_sequence: GCCAAT + tag_set_id_lims: 27 + tag_set_name: 'TruSeq mRNA Adapter and NEB Small RNA Index Sequences - 6mer' + team: Illumina-C + workflow: ~ + diff --git a/t/data/run_params/RunParameters.novaseqx.onboard.xml b/t/data/run_params/RunParameters.novaseqx.onboard.xml new file mode 100644 index 00000000..0a072c63 --- /dev/null +++ b/t/data/run_params/RunParameters.novaseqx.onboard.xml @@ -0,0 +1,79 @@ + + + B + control-software + 1.1.0.18335 + 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