Bump version to 4.0.0

[Aratz]

[4.0.0] - 2026-05-19

Added

• Add Proxiome V2 workflow support, enabling sample pooling and processing of up to 8,000 cells per run by @Aratz #204, #205

Enhancements & fixes

• Use nextflow strict syntax by @Aratz #194
• Use TMPDIR when defined to store temporary files by @Aratz #195
• Retry experiment summary up to two times after failure by @Aratz #196
• Updated pixelatorES to 0.10.1 in PNA experiment summary step by @Aratz #197, #204
• Add cells_1k and cells_8k Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg #202

Software dependencies

Dependency	Old version	New version
pixelatorES	0.6.0	0.10.1
pixelator	0.23.0	0.26.0

Warning

Panel and design names have been completely renamed in pixelator 0.26 (nf-core/pixelator 4.0 and above). Refer to the pixelator changelog for more details.

Parameters

Old parameter	New parameter
--leiden-iterations
--min-component-size-in-refinement
--min-component-size-to-prune
	--edge_cycle-verification

Note

Parameter has been updated if both old and new parameter information is present.
Parameter has been added if just the new parameter information is present.
Parameter has been removed if new parameter information isn't present.