QIIME 2 2025.4 breaking changes & environment files

Announcements
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Hello QIIME 2 Developer community! :nerd_face::wave:t3:

Below is the list of guaranteed interface changes, plugin API changes, and environment file updates for the 2025.4 QIIME 2 release. You can use the linked environment files for each distribution to ensure compatibility with any plugin you're developing against the relevant distribution it should be tested/used within. Note that these 'seed' environment files won't change between now and the 2025.4 release, but the full environment files that conda will resolve at any given installation will change. This shouldn't impact your development process, as all of the core dependencies in these 'seed' files will remain the same.

Interface Changes :tv:

  • q2-dada2
    • The pooled option to the --p-chimera-method parameter was removed as it should only be used in tandem with other parameter options that are not available in QIIME2.

Plugin API Changes :electric_plug:

Environment File Changes :card_file_box:

NOTE: The metagenome distribution has been renamed to moshpit!

  • tiny
    • biom-format has been bumped to 2.1.16
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
  • amplicon
    • rpy2 has been added as a new external dependency to support the new ANCOM-BC2 wrapper within q2-composition
    • biom-format has been bumped to 2.1.16
    • fastp 0.24.0 has been added as a new dependency for future functionality in amplicon and moshpit distributions
    • r-vegan has been bumped to 2.6_8
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
    • vsearch 2.22.1 has been added as a new dependency to match the existing pins in moshpit and pathogenome
  • moshpit
    • q2-alignment has been added as a new QIIME 2 dependency, as RESCRIPt now depends on it.
    • q2-moshpit has been renamed to q2-annotate
    • biom-format has been bumped to 2.1.16
    • fastp 0.24.0 has been added as a new dependency for future functionality in amplicon and moshpit distributions
    • mafft has been pinned at 7.526 due to second order dependencies
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
    • spades has been bumped to 4.0.0
  • pathogenome
    • biom-format has been bumped to 2.1.16
    • mafft has been pinned at 7.526 due to second order dependencies
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
    • spades has been bumped to 4.0.0
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2 off-topic replies have been split into a new topic: the pooled option to the --p-chimera-method parameter in q2-dada2

Please keep replies on-topic in the future.