Fix custom/resolvetaxonomy: malformed output filename for extensionless input - #12824
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erikrikarddaniel merged 1 commit intoAug 26, 2026
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sequences.extension is '' (not the more Groovy-idiomatic null) when the
input file has no extension at all -- e.g. a download URL whose path is
just a numeric file id, with no filename suffix. That produced a
malformed "${prefix}.resolved." output name (matching nothing downstream)
instead of a real file.
Found while wiring this module into nf-core/phyloplace: its phylosearch
test samplesheet has exactly such a refseqfile (a Figshare download URL).
Fix falls back to 'fasta' via sequences.extension ?: 'fasta', inline in
the output declaration -- output: patterns can only reference input-bound
variables directly, not script:-scoped def locals (confirmed empirically:
using a def from script: in the output: block is a compile-time error,
"`ext` is not defined"), so the fallback is duplicated inline in script:,
stub: and the output: glob itself rather than shared via one variable.
Generated by Claude
erikrikarddaniel
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August 26, 2026 17:09
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…ss-input filename)
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PR checklist
topic: versions- See version_topicsnf-core modules test custom/resolvetaxonomy --profile dockernf-core modules test custom/resolvetaxonomy --profile singularitynf-core modules test custom/resolvetaxonomy --profile condaDescription
Found while wiring
custom/resolvetaxonomy(merged in #12817) into nf-core/phyloplace: itssequencesoutput is named"*.resolved.${sequences.extension}", butPath.extensionis''(not null) when the input file has no extension at all -- e.g. a bare download URL whose path is just a numeric file id (.../files/47244067, no filename suffix). That produced a malformed"${prefix}.resolved."output name, matching nothing, so the process silently failed to produce a usablesequencesoutput.Fix: fall back to
'fasta'viasequences.extension ?: 'fasta'.One thing worth flagging for other module authors: I first tried factoring this into a single
def ext = sequences.extension ?: 'fasta'in thescript:block and reusing${ext}in theoutput:declaration (the same patterndef prefix = task.ext.prefix ?: ...uses everywhere) -- that's a compile-time error,`ext` is not defined.output:glob patterns can only reference input-bound variables (sequences,meta, etc.) directly, notscript:-scopeddeflocals. Confirmed this empirically rather than assuming from theprefixprecedent, sinceprefixitself is only ever used inscript:/stub:, never in anoutput:pattern, in this module or apparently elsewhere. So the fallback is duplicated inline inscript:,stub:and theoutput:glob itself.Added a test case with a synthesized extension-less input file (no new fixture needed -- built inline in the test from the existing
resolvetaxonomy_embedded.fastafixture) covering the regression.Ran
nf-test test modules/nf-core/custom/resolvetaxonomy --profile docker(8/8 passing, including the new case) twice to confirm stability, andnf-core modules lint custom/resolvetaxonomy(clean). Docker only -- I have not run the singularity or conda profiles.Generated by Claude