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Rename source and source_version datasheet meta fields - #166
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The datasheet fields were renamed upstream in references-datasheets #22, so this aligns the schema and every consumer of the meta map: - source becomes reference_source, in the schema field and meta array, reduceMeta, and 27 publish paths - source_version becomes annotation_version, including the NCBI download grouping key at main.nf that carries the assembly accession - the derived source_vcf record becomes annotation_source; the vcf_*_source datasheet fields it reads keep their names Caught by 24 of 27 tests failing against the live latest branch: missing source rendered an empty list into publish paths while runs reported success, and missing source_version fell back to the schema default unknown, which NCBI rejected as an assembly accession. Generated by OpenCode
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PR checklist
CHANGELOG.mdis updatednextflow_schema.jsonis updated (if needed)docs/usage.mdis updated (if needed)docs/output.mdis updated (if needed)assets/is updated (if needed)TODOcommentsDescription
Completes #65 by aligning this pipeline with the datasheet field renames merged upstream in
nf-core/references-datasheets(#22):sourcereference_sourcereduceMeta, 27 publish pathssource_versionannotation_versionreduceMeta, 6 sites including the NCBI grouping keysource_vcf(derived meta only)annotation_sourcetoVcfChannelrecord, one publish pathThe
vcf_*_sourcedatasheet fields keep their names: they label one resource's provenance (GATKBundle), not the whole entry. The schema fieldsource_versiondefault ofunknownalso stays, since it guards datasheets that never carried the field.Docs examples follow the rename:
README.md,docs/usage.md, and the published path pattern indocs/CONTRIBUTING.md.Why now
The upstream rename went live on the
latestbranch that these tests read, and 24 of 27 tests failed against it in two shapes:sourcerendered an empty list into publish paths, so runs published intoHomo_sapiens/[]/GRCh37/...while reporting success. Only the snapshot path assertions caught it.source_versionfell back to the schema defaultunknown, which became the NCBI assembly accession:datasets download genome accession unknown, failing outright in the E.Coli and WBCEL235 tests.This PR closes that window.
Known looseness
For NCBI datasheets
annotation_versioncarries an assembly accession (GCF_000005845.2) rather than an annotation release, because the NCBI download groups by that value. The name was chosen before this surfaced, and it is now locked by the merged upstream rename, so reopening it would cost a second cross-repo sweep for a partial mismatch.ro-crate-metadata.jsonis untouched: it is generated and must not be edited by hand.Testing
nextflow lint: no errors (23 warnings, all pre-existingwhen-section deprecations in nf-core modules).prek: passes, twice, with no fixers touching the staged files.nf-test test tests/ --profile=+docker: 27/27 passing (898s), including the NCBI trio that failed onunknownaccessions and the substitution test that failed on its fixture