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Add taxonomytree_test fixtures for custom/taxonomytree module tests - #2274

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erikrikarddaniel merged 1 commit into
nf-core:modulesfrom
erikrikarddaniel:modules
Sep 16, 2026
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erikrikarddaniel merged 1 commit into
nf-core:modulesfrom
erikrikarddaniel:modules

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PR checklist

Needed by nf-core/modules#12977 (custom/taxonomytree module + taxonomy2phylogeny subworkflow).

  • I read the test-data specifications
  • I tried testing my module with available data and there is no compatible data in test-datasets
  • If I added data: I described the new files on the root README.md
  • If I modified data: I checked whether the root README.md is still up-to-date
  • I made sure to submit the smallest dataset possible (e.g. try .tar.gz for larger directories)

Description

Two small fixtures for custom/taxonomytree and taxonomy2phylogeny tests in
nf-core/modules#12977:

  • data/generic/tax/taxonomytree_test.tax: 6 samples' taxonomy strings.
  • data/generic/fasta/taxonomytree_test.fasta: matching 6 synthetic 61bp DNA sequences with
    real phylogenetic signal (three shared-mutation pairs).

6 taxa, not 4: a 4-taxon taxonomy-derived guide tree is always fully resolved (any grouping on
4 leaves already needs the one internal split an unrooted 4-taxon tree has), which
raxml-ng --tree-constraint correctly rejects as "not a real constraint" -- confirmed by
hitting that exact rejection with an earlier 4-taxon draft. 6 taxa (one resolved pair, a 3-way
polytomy, and a second resolved pair under a different kingdom) gives a genuine, still-unresolved
constraint, needed to test the guide-tree-as-constraint wiring for real.

🤖 Generated with Claude Code

https://claude.ai/code/session_014eSqkuYZXfNiWy87y3srup

@erikrikarddaniel
erikrikarddaniel merged commit f60a843 into nf-core:modules Sep 16, 2026
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2 participants