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feat(spikeinterface/sort): add module wrapping SpikeInterface 0.101.2 spike sorting#11464

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feat(spikeinterface/sort): add module wrapping SpikeInterface 0.101.2 spike sorting#11464
olaflaitinen wants to merge 1 commit intonf-core:masterfrom
olaflaitinen:spikeinterface-sort

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@olaflaitinen olaflaitinen commented May 3, 2026

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, have you added tests?
  • If necessary, have you added documentation to the README.md in the module/subworkflow directory?
  • If you've added a new tool, have you added its information to the modules meta.yml file?
  • If you've added a new tool, have you added the tool name to tags.yml?
  • If you've added a new modules, have you added each module to every tags.yml category it fits in?
  • If you've added a new pipeline, have you added each tool to tags.yml for the categories it fits into?
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-core test or nf-test where applicable).
  • Use Conventional Commit messages (feat:, fix:, etc.).
  • If this is a workflow / subworkflow change, have you updated documentation in the docs/ directory?
  • If you've added a module, have you added CI tests for the module to tests/pytest/test_modules.py?

Description

Adds spikeinterface/sort, a process module wrapping SpikeInterface 0.101.2 for extracellular spike sorting. Conda package is pinned as conda-forge::spikeinterface=0.101.2 (build reflected in Multi-container tag pyh0610db2_0). Container uses biocontainers/spikeinterface:0.101.2--pyh0610db2_0.

versions.yml records spikeinterface: 0.101.2 and spike_sorter: <sorter channel> so snapshots remain stable across runs.

biotools identifier: biotools:spikeinterface.

Outstanding follow-ups

  1. Add modules/data/genomics/electrophysiology/recording_small.bin under nf-core/test-datasets (HTTP 404 as of validation). Candidate: attach a minimal public-domain or CC0-compatible int16 extracellular excerpt (single channel, 30 kHz) under 5 MB, then rerun nf-test --update-snapshot so the integration test MD5 placeholders in tests/main.nf.test.snap are replaced.

  2. nf-core modules lint reports transient container registry warnings (Quay HEAD 403 / Galaxy depot 404 for this tag in the lint environment). Consider a Wave URL once available or a depot-published Singularity artifact if the nf-core bots provide one.

… spike sorting

Co-authored-by: Cursor <cursoragent@cursor.com>
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