Update pixelator to 0.29.0#227
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…s with updated data" This reverts commit 40dc85f.
Aratz
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Jun 22, 2026
Aratz
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Looks great, nice work with the tests!
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Looking at the changes I realized the next pipeline version will probably have to be 5.0.0 if we want to stick to semantic versioning 🥲
From https://nf-co.re/docs/specifications/pipelines/requirements/semantic_versioning:
Major Release (e.g., 1.4.3 to 2.0.0)
Changes that are not backwards compatible and may require users to adjust their existing workflows or configurations.
Breaking Changes:
- ...
- Renaming or deprecation of existing parameter(s).
- ...
- Upgrades to dependencies that introduce breaking changes. For example if the new version of the tool requires additional parameters, removes parameters passed by the pipeline, or changes its outputs in a way that necessitates changes to module output definitions.
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Summary
Updates the pipeline to pixelator 0.29.0 and pixelatorES 0.11.2, aligning parameters, tests, and snapshots with upstream API and behaviour changes. Includes a coordinated refresh of PNA v2 test fixtures (pool-level denoise, prerelease panel).
Container / dependency updates
PIXELATOR_*modules from 0.28.0 → 0.29.0EXPERIMENT_SUMMARY(pixelatorES) from 0.10.4 → 0.11.2proxiome-v2-immuno-155-prereleaseto thePIXELATOR_LIST_OPTIONSstub panel listParameter & schema changes
pna_sample_calling_confidence_threshold→pna_sample_calling_enrichment_thresholdand wire--enrichment-thresholdinconf/modules.pna.config(default is 10.0, pixelator 0.29.0 default)wpmds_3d→coarsened_pmds_3d(pixelator 0.29.0 default); addcoarsened_pmds_3dto schema enum/defaultnextflow_schema.jsondefaults and descriptions accordinglyTest profile behaviour
test_proxiome_v1.config/test_proxiome_v2.config: override layout towpmds_3dfor CI/minimal testsSynthetic nf-core test data still contains graph components too small for
coarsened_pmds_3d+ default--pmds-pivots 50; production default remainscoarsened_pmds_3dproxiome-v2-immuno-155-prereleaseEXPERIMENT_SUMMARYmodule test: update denoise fixtures from sample-level (sample1–sample4) to pool-level (pool1,pool2) to match v2 pipeline behaviour and pixelatorES 0.11.2 expectations (i.e do denoise before sample calling)PIXELATOR_LAYOUTmodule test: usepna_layout_layout_algorithm = "coarsened_pmds_3d"(fixes previously ignoredlayout_algorithmparam)Related PRs
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).