Only pass --expansion-distance for nuclei-based xeniumranger imports

[rnaidu-seqera]

Problem

xeniumranger import-segmentation fails on transcript-based segmentation methods:

ERROR: --expansion-distance requires --nuclei.
Error executing process > 'NFCORE_SPATIALAXE:SPATIALAXE:PROSEG_PRESET_PROSEG2BAYSOR:XENIUMRANGER_IMPORT_SEGMENTATION (test_run)'

Reproducible with -profile test (which enables transcript_seg_methods = [proseg, segger, baysor]).

Root cause

conf/modules.config applied --expansion-distance to every XENIUMRANGER_IMPORT_SEGMENTATION invocation via withName. But xeniumranger only accepts --expansion-distance for nuclei-based imports — it expands nuclei outward into cell boundaries. The import step runs in two mutually-exclusive modes (enforced by the module itself):

• nuclei/cells (--nuclei / --cells) — image segmentation
• transcript assignment (--transcript-assignment + --viz-polygons) — proseg / baysor / segger

The transcript-assignment methods pass nuclei = [], so --expansion-distance is invalid there and xeniumranger rejects it. (The same applies to the cells-only import in xeniumranger_resegment_morphology_ome_tif.)

This isn't exercised by CI because xeniumranger is a licensed tool that CI can't run.

Fix

Gate --expansion-distance on the module's nuclei input, so it is emitted only when a nuclei segmentation is being imported — matching xeniumranger's own rule:

(nuclei && params.expansion_distance != null) ? "--expansion-distance=${params.expansion_distance}" : ""

Config-only; no change to the shared nf-core module. Preserves the flag for the genuine nuclei imports (stardist / cellpose), and removes it where the tool forbids it (transcript-assignment and cells-only imports).

Validation

• Confirmed an ext.args closure can reference the module's nuclei path input, and that it resolves correctly among the module's other path inputs.
• Truthiness verified for the real input types: empty input (nextflow.util.BlankSeparatedList, size 0) → flag omitted; staged path (nextflow.processor.TaskPath) → flag emitted.
• nextflow lint passes.

PR checklist

• CHANGELOG.md is updated.
• Documentation update (n/a — no user-facing parameter/behaviour change).
• nf-test / CI green (please run in nf-core CI; note this path needs the licensed xeniumranger tool to exercise end-to-end).

[heylf]

LGTM. Thank you @rnaidu-seqera for your help!