Test Profile fails at import segmentation

[tylerstahl]

Description of the bug

We are running the test profile and encountered this error at the Xenium import segmentation step. Based on the error message, --expansion-distance shouldn't be assigned or a nuclei image needs to be provided via --nuclei.

Command used and terminal output

nextflow run nf-core/spatialaxe -r 1.0.0 -profile test --outdir results -c test.config

Relevant files

Snippet from the .nextflow.log

Command executed:

  xeniumranger import-segmentation \
      --id="XENIUMRANGER_IMPORT_SEGMENTATION" \
      --xenium-bundle="bundle/test_run" \
      --localcores=4 \
      --localmem=8 \
      --expansion-distance=5 \
      --transcript-assignment="transcript-metadata.csv" \
      --viz-polygons="cell-polygons.geojson" \
      --units="microns"
  
  rm -rf "test_run"
  mv XENIUMRANGER_IMPORT_SEGMENTATION/outs "test_run"

Command exit status:
  1

Command output:
  ERROR: --expansion-distance requires --nuclei.

Additional config passed to the nextflow run command:

process {
  scratch = false
}

System information

Nextflow version: 26.04.0
Hardware: HPC
Executor: SLURM
Container engine: Singularity
OS: Linux
Version of nf-core/spatialaxe: 1.0.0

[khersameesh24]

Hi @tylerstahl , thanks for reporting the error. This was fixed last week in a PR that is up for review. We will have a release version soon with minor changes to fix this and other issues we have identified.

here is the link :
https://github.com/nf-core/spatialaxe/pull/184/changes#diff-bf809c928cb10b54d251dec8a140a2d5505150f97175d8d7b51dda9cc57971feR86