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dnaseq Experiment #108

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34 changes: 33 additions & 1 deletion Model/lib/xml/datasetClass/classes.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7085,6 +7085,37 @@ where e.na_sequence_id = ns.na_sequence_id and ns.external_database_release_id =
</datasetLoader>
</datasetClass>

<!-- New dataset class replacing dnaSeqExperimentFromAccession and dnaSeqExperimentFromLocal.
Uses nf-core samplesheet convention; fromSRA and ploidy are per-dataset props.
taxonId is looked up at runtime from the DB in MakeDnaSeqNextflowConfig. -->
<datasetClass class="dnaseqExperiment" category="" datasetFileHint="">
<purpose></purpose>
<prop name="projectName">&projectName;</prop>
<prop name="organismAbbrev">&organismAbbrev;</prop>
<prop name="name">&name;</prop>
<prop name="version">&version;</prop>
<prop name="fromSRA"></prop>
<prop name="ploidy"></prop>
<graphTemplateFile name="dnaseq.xml"/>
<datasetLoader datasetName="${organismAbbrev}_${name}_dnaseqExperiment_RSRC" version="${version}"
plugin="ApiCommonData::Load::Plugin::LoadNothing"
scope="organism"
type="isolates"
subType="Dna_Seq"
organismAbbrev="${organismAbbrev}">
<manualGet fileOrDir="common/empty">
<dir name="final">
</dir>
</manualGet>
<unpack>ln -s @@manualDeliveryDir@@/${projectName}/${organismAbbrev}/dnaSeq/${name}/${version}/final/ @@dataDir@@/final</unpack>
<getAndUnpackOutput dir="@@dataDir@@/final"/>
<getAndUnpackOutput file="@@dataDir@@/final/samplesheet.csv"/>
<pluginArgs>--dbRefExternalDatabaseSpec "%DATASET_NAME%|%DATASET_VERSION%"</pluginArgs>
</datasetLoader>
</datasetClass>

<!-- DEPRECATED - replaced by dnaseqExperiment above.
Retain until all organism dataset XMLs are migrated. -->
<datasetClass class="dnaSeqExperimentFromAccession" category="" datasetFileHint="">
<purpose></purpose>
<prop name="projectName">&projectName;</prop>
Expand Down Expand Up @@ -7115,7 +7146,8 @@ where e.na_sequence_id = ns.na_sequence_id and ns.external_database_release_id =

</datasetClass>


<!-- DEPRECATED - replaced by dnaseqExperiment above.
Retain until all organism dataset XMLs are migrated. -->
<datasetClass class="dnaSeqExperimentFromLocal" category="" datasetFileHint="">
<purpose></purpose>
<prop name="projectName">&projectName;</prop>
Expand Down