Add fixtures for custom/resolvetaxonomy module tests - #2239
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erikrikarddaniel merged 1 commit intoAug 26, 2026
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Small hand-authored FASTA/tax pairs covering the module's three taxonomy sources (embedded header text, explicit file, neither) for both nf-core/sativa and nf-core/phyloplace, which are adopting this as a shared module. Generated by Claude
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The fasta/ and tax/ fixtures added for custom/resolvetaxonomy tests in nf-core#2239 were never added to the Data Description section. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH
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Description
Small hand-authored fixtures for the new
custom/resolvetaxonomymodule (nf-core/modules, PR to follow) -- a shared module that resolves a set of sequences' taxonomy either from an explicit tab-separated taxonomy file or, if omitted, from embedded GTDB-style taxonomy text in each FASTA header (>id taxonomy;string). It's a generalisation of nf-core/sativa's existing localresolvetaxonomymodule, being adopted by nf-core/phyloplace as well.Five small files under
data/generic/fasta/anddata/generic/tax/, covering the module's three taxonomy sources:resolvetaxonomy_embedded.fasta-- two records with embedded header taxonomy, no external file.resolvetaxonomy_override.tax-- an explicit taxonomy file with different lineages than the embedded text above, to test that an explicit file wins (with a warning).resolvetaxonomy_plain.fasta/resolvetaxonomy_plain.tax-- records with no embedded text, paired with a plain explicit taxonomy file (no warning expected), and reused on their own to test the "neither source available" path.resolvetaxonomy_partial.fasta-- one record with embedded taxonomy, one without, to test the module's non-required mode (drops the record with no taxonomy, with a warning, instead of failing the whole run).Generated by Claude