[update] xeniumranger import segemtnation - #12421
Merged
Merged
Conversation
mashehu
approved these changes
Jul 24, 2026
mashehu
approved these changes
Jul 24, 2026
mashehu
reviewed
Jul 27, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Add
expansion_distanceparameter to xeniumranger/import-segmentationWhat changed
expansion_distanceinput: the module now accepts anexpansion_distancevalue (integer, microns) in the input tuple and passes it toxeniumranger as
--expansion-distance=<value>when provided.nuclei: the flag is only emitted when anucleisegmentation fileis also supplied. xeniumranger rejects
--expansion-distancefortranscript-assignment imports (proseg/baysor/segger) and cells-only imports, since
expansion only makes sense when expanding nuclei into cell boundaries.
nf-testcases intests/main.nf.testnow pass5as theexpansion_distanceargument to match the new process input signature.Why
--expansion-distancecontrols how far nuclei are expanded outward to approximatecell boundaries, so it only applies to nuclei-based imports. Passing it unconditionally
would break transcript-assignment and cells-only import runs, since xeniumranger
errors out when the flag is used without
--nuclei. Making the flag conditional keepsall three import modes working from a single process definition.
Testing
nf-testsnapshot tests inmodules/nf-core/xeniumranger/import-segmentation/tests/main.nf.testto supply thenew
expansion_distancevalue, keeping them in sync with the updated input tuple.Files changed
modules/nf-core/xeniumranger/import-segmentation/main.nfmodules/nf-core/xeniumranger/import-segmentation/meta.ymlmodules/nf-core/xeniumranger/import-segmentation/tests/main.nf.testPR checklist
Linked to issue: nf-core/spatialaxe issue #186
labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularity