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Distinguish between NovaSeq and NovaSeqX RunParams. #777

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merged 2 commits into from
Nov 17, 2023
Merged

Distinguish between NovaSeq and NovaSeqX RunParams. #777

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7a25f37
Distinguish between NovaSeq and NovaSeqX RunParams.
mgcam Nov 17, 2023
1bdc279
More robust evaluation.
mgcam Nov 17, 2023
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1 change: 1 addition & 0 deletions MANIFEST
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Original file line number Diff line number Diff line change
Expand Up @@ -666,6 +666,7 @@ t/data/run_params/runParameters.hiseqx.upgraded.xml
t/data/run_params/runParameters.hiseqx.xml
t/data/run_params/runParameters.miseq.xml
t/data/run_params/RunParameters.novaseq.xp.lite.xml
t/data/run_params/RunParameters.novaseqx.prod.xml
t/data/samplesheet/samplesheet_7753.csv
t/data/samplesheet/samplesheet_27483.csv
t/data/samplesheet/samplesheet_33990.csv
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3 changes: 2 additions & 1 deletion lib/npg_tracking/illumina/run/long_info.pm
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Expand Up @@ -592,7 +592,8 @@ instrument belonging to NovaSeq platform.

sub platform_NovaSeq {
my $self = shift;
return $self->_software_application_name() =~ /NovaSeq/xms;
return (!$self->platform_NovaSeqX() &&
($self->_software_application_name() =~ /NovaSeq[ ]/xms));
}

=head2 platform_NovaSeqX
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12 changes: 8 additions & 4 deletions t/60-illumina-run-long_info.t
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Expand Up @@ -29,7 +29,7 @@ package main;
my $basedir = tempdir( CLEANUP => 1 );

subtest 'retrieving information from runParameters.xml' => sub {
plan tests => 167;
plan tests => 177;

my $rf = join q[/], $basedir, 'runfolder';
mkdir $rf;
Expand All @@ -52,7 +52,8 @@ subtest 'retrieving information from runParameters.xml' => sub {
RunParameters.novaseq.xp.xml
RunParameters.novaseq.xp.v1.5.xml
runParameters.hiseq.rr.truseq.xml
RunParameters.novaseqx.xml
RunParameters.novaseqx.xml
RunParameters.novaseqx.prod.xml
/;
my $dir = 't/data/run_params';

Expand Down Expand Up @@ -117,8 +118,11 @@ subtest 'retrieving information from runParameters.xml' => sub {
} else {
ok (!$li->uses_patterned_flowcell, 'not patterned flowcell');
}

ok (!$li->onboard_analysis_planned(), 'onboard analysis is not planned');
if ($f =~ /novaseqx\.prod/) {
ok ($li->onboard_analysis_planned(), 'onboard analysis is planned');
} else {
ok (!$li->onboard_analysis_planned(), 'onboard analysis is not planned');
}

unlink $name;
}
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87 changes: 87 additions & 0 deletions t/data/run_params/RunParameters.novaseqx.prod.xml
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@@ -0,0 +1,87 @@
<?xml version="1.0" encoding="utf-8"?>
<RunParameters xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<Side>B</Side>
<Application>NovaSeqXSeries Control Software</Application>
<SystemSuiteVersion>1.2.0.26276</SystemSuiteVersion>
<OutputFolder>//nx2-esa.dnapipelines.sanger.ac.uk/staging/IL_seq_data/incoming/20231019_LH00275_0006_B19NJCA4LE</OutputFolder>
<CloudUploadMode>InstrumentPerformance</CloudUploadMode>
<RunSetupMode>LocalOrchestrated</RunSetupMode>
<SecondaryAnalysisMode>LocalAnalysis</SecondaryAnalysisMode>
<InstrumentType>NovaSeqXPlus</InstrumentType>
<InstrumentSerialNumber>LH00275</InstrumentSerialNumber>
<RunId>20231019_LH00275_0006_B19NJCA4LE</RunId>
<RunCounter>6</RunCounter>
<RecipeName>25B Sequencing</RecipeName>
<RecipeVersion>25B-01.02.00</RecipeVersion>
<ExperimentName>47999_NX2_B</ExperimentName>
<FlowCellName>NovaSeqXSeries B4</FlowCellName>
<FlowCellType>NovaSeqXSeriesB4</FlowCellType>
<ConsumableInfo>
<ConsumableInfo>
<SerialNumber>19NJCA4LE</SerialNumber>
<LotNumber>9345L1E1</LotNumber>
<PartNumber>20088038</PartNumber>
<ExpirationDate>2024-04-29T00:00:00+01:00</ExpirationDate>
<Type>FlowCell</Type>
<Mode>4</Mode>
<Version>1.0</Version>
<Name>25B</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC2305090085-1</SerialNumber>
<LotNumber>23050901</LotNumber>
<PartNumber>20089853</PartNumber>
<ExpirationDate>2024-08-09T00:00:00+01:00</ExpirationDate>
<Type>Buffer</Type>
<Mode>3</Mode>
<Version>1.0</Version>
<Name>Universal</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC1001941-LS1</SerialNumber>
<LotNumber>1000018698</LotNumber>
<PartNumber>20101913</PartNumber>
<ExpirationDate>2025-08-25T00:00:00+01:00</ExpirationDate>
<Type>SampleTube</Type>
<Mode>3</Mode>
<Version>1.0</Version>
<Name>8 Lane</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC4044182-25B3</SerialNumber>
<LotNumber>20784608</LotNumber>
<PartNumber>20066626</PartNumber>
<ExpirationDate>2024-08-20T00:00:00+01:00</ExpirationDate>
<Type>Reagent</Type>
<Mode>4</Mode>
<Version>1.5</Version>
<Name>25B 300c</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC2000520-LI5</SerialNumber>
<LotNumber>17792769</LotNumber>
<PartNumber>20090674</PartNumber>
<ExpirationDate>2024-05-11T00:00:00+01:00</ExpirationDate>
<Type>Lyo</Type>
<Mode>11</Mode>
<Version>1.5</Version>
<Name>High</Name>
</ConsumableInfo>
</ConsumableInfo>
<PlannedReads>
<Read ReadName="Read1" Cycles="151" />
<Read ReadName="Index1" Cycles="8" />
<Read ReadName="Index2" Cycles="8" />
<Read ReadName="Read2" Cycles="151" />
</PlannedReads>
<SecondaryAnalysisInfo>
<SecondaryAnalysisInfo>
<SecondaryAnalysisPlatformVersion>4.1.7</SecondaryAnalysisPlatformVersion>
<SecondaryAnalysisWorkflow>
<string>DRAGEN BCL Convert</string>
<string>DRAGEN Germline</string>
</SecondaryAnalysisWorkflow>
</SecondaryAnalysisInfo>
</SecondaryAnalysisInfo>
<DisableBclCopy>false</DisableBclCopy>
</RunParameters>