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Scrnaseq updates#98

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jmvera255 merged 20 commits into
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scrnaseq-updates
Jun 22, 2026
Merged

Scrnaseq updates#98
jmvera255 merged 20 commits into
mainfrom
scrnaseq-updates

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@jmvera255

@jmvera255 jmvera255 commented Jun 22, 2026 •
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  • refine conditional behavior for scRNA-seq Assay metadata collection related to specimenModality
  • refine attributes, expand enums, and eliminate redundancy related to scRNA-seq assay types and alignment references to better support metadata collection for 10x Flex data
  • rename fcs context to cytometry to reflect expanded use cases
  • overhaul/eliminate conditional behaviors linked to specimenModality
    • have single upsert/primary key attribute for existing assay metadata collection templates
  • expand/harmonize enums for libraryPrepMethod and platform

jmvera255 and others added 20 commits June 22, 2026 12:38
@jmvera255
remove 10xCustomProbeSet and related attributes, instead use alignmen…
e376707 
…tReference and modified conditional behavior to improve metadata collection
@jmvera255
rename context to reflect expanded context applications including Ass…
f680a70 
…ayMetadataTemplates for cytometry-based data
@jmvera255
Merge f680a70 into 42b0a0e
2fe50dd
@jmvera255
GitHub Action: commit results of ci-schema-convert workflow
2e323ce
@jmvera255
convert class/type of nucleicAcidSource from STRINGLIST to just STRING
7c6e0b7
@jmvera255
add biospecimenID to dependsOn for all Assay metadata templates b/c …
4554672 
…of change in conditional behavior related to specimenModality; fix conditional behavior for customAlignmentReferenceSynID to produce expected behavior
@jmvera255
Merge 4554672 into 42b0a0e
7617d0f
@jmvera255
GitHub Action: commit results of ci-schema-convert workflow
700fa8f
@jmvera255
add libraryID to dependsOn for assay metadata now that conditional de…
fd6a14e 
…pendency related to specimenModality has changed
@jmvera255
expand and harmonize enums for alignmentReference
2232ff0
@jmvera255
expand and harmonize enums for libraryPrepMethod
4dd394a
@jmvera255
Merge 4dd394a into 42b0a0e
d2039d9
@jmvera255
GitHub Action: commit results of ci-schema-convert workflow
70a830a
@jmvera255
minor description revision to be more instructive
4a82dac
@jmvera255
remove 10x Chromium chips and instruments from 'platform' enums, set …
0b95160 
…to just string instead of STRINGLIST as I think this is confusing for the contributors
@jmvera255
remove conditional behavior connected to specimenModality in favor of…
8582f8a 
… always collecting libraryID which is now always required in assay metadata templates for sequencing-based assays
@jmvera255
remove conditional behavior connected to specimenModality in favor of…
86d6de3 
… always collecting slideID which is now always required in assay metadata template
@jmvera255
Merge 86d6de3 into 42b0a0e
820eb93
@jmvera255
GitHub Action: commit results of ci-schema-convert workflow
b2e99f9
@jmvera255
Merge b2e99f9 into 42b0a0e
137a22e
@jmvera255 jmvera255 merged commit 7e51c42 into main Jun 22, 2026
@jmvera255 jmvera255 deleted the scrnaseq-updates branch June 23, 2026 17:27
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@jmvera255