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dnaseq Experiment #108

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dnaseq Experiment #108

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8311a42
Add dnaseqExperiment dataset class; deprecate old dnaSeq classes
jbrestel Apr 5, 2026
95cb5d9
rm extra dnaseq dataset classes
jbrestel May 15, 2026
d4fd31b
for dnaseqExperiment, change manual delivery dir from ${organismAbbre…
sufenhu May 18, 2026
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51 changes: 10 additions & 41 deletions Model/lib/xml/datasetClass/classes.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7085,67 +7085,36 @@ where e.na_sequence_id = ns.na_sequence_id and ns.external_database_release_id =
</datasetLoader>
</datasetClass>

<datasetClass class="dnaSeqExperimentFromAccession" category="" datasetFileHint="">
<!-- 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="isPaired"></prop>
<prop name="fromSRA"></prop>
<prop name="ploidy"></prop>
<prop name="fromBAM"></prop>
<prop name="isLocal"></prop>
<prop name="taxonId"></prop>
<graphTemplateFile name="dnaseq.xml"/>

<datasetLoader datasetName="${organismAbbrev}_dnaseqExperiment_${name}_RSRC" version="${version}"
<datasetLoader datasetName="${organismAbbrev}_${name}_dnaseqExperiment_RSRC" version="${version}"
plugin="ApiCommonData::Load::Plugin::LoadNothing"
scope="organism"
type="isolates"
subType="Dna_Seq"
organismAbbrev="${organismAbbrev}">
<manualGet fileOrDir="${projectName}/${organismAbbrev}/dnaSeq/${name}/${version}/final/accessions.tsv">
<manualGet fileOrDir="common/empty">
<dir name="final">
</dir>
</manualGet>
<getAndUnpackOutput file="@@dataDir@@/accessions.tsv"/>

<unpack>ln -s @@manualDeliveryDir@@/${projectName}/${organismAbbrev}/SNP/${name}/${version}/final/ @@dataDir@@/final</unpack>
<getAndUnpackOutput dir="@@dataDir@@/final"/>
<getAndUnpackOutput file="@@dataDir@@/final/samplesheet.csv"/>
<pluginArgs>--dbRefExternalDatabaseSpec "%DATASET_NAME%|%DATASET_VERSION%"</pluginArgs>
</datasetLoader>

</datasetClass>


<datasetClass class="dnaSeqExperimentFromLocal" 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="isPaired"></prop>
<prop name="ploidy"></prop>
<prop name="fromBAM"></prop>
<prop name="isLocal"></prop>
<prop name="taxonId"></prop>
<graphTemplateFile name="dnaseq.xml"/>

<datasetLoader datasetName="${organismAbbrev}_dnaseqExperiment_${name}_RSRC" version="${version}"
plugin="ApiCommonData::Load::Plugin::LoadNothing"
scope="organism"
type="isolates"
subType="Dna_Seq"
organismAbbrev="${organismAbbrev}">
<manualGet fileOrDir="${projectName}/${organismAbbrev}/dnaSeq/${name}/${version}/final/">
<dir name="final">
</dir>
</manualGet>
<getAndUnpackOutput file="@@dataDir@@/final"/>

<pluginArgs>--dbRefExternalDatabaseSpec "%DATASET_NAME%|%DATASET_VERSION%"</pluginArgs>
</datasetLoader>

</datasetClass>

<!-- New dataset class for the long read RNA Seq -->
<datasetClass class="longReadRnaSeqExperiment" category="" datasetFileHint="">
<purpose></purpose>
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