[update] xeniumranger import segemtnation

.github/skip_nf_test.json

@@ -107,7 +107,7 @@
         "modules/nf-core/universc",
         "modules/nf-core/vt/decompose",
         "modules/nf-core/wittyer",
-        "modules/nf-core/xeniumranger/import-segmentation",
+        "modules/nf-core/xeniumranger/importsegmentation",
         "modules/nf-core/xeniumranger/relabel",
         "modules/nf-core/xeniumranger/rename",
         "modules/nf-core/xeniumranger/resegment",

modules/nf-core/xeniumranger/import-segmentation/main.nf → modules/nf-core/xeniumranger/importsegmentation/main.nf

@@ -1,11 +1,11 @@
-process XENIUMRANGER_IMPORT_SEGMENTATION {
+process XENIUMRANGER_IMPORTSEGMENTATION {
     tag "$meta.id"
     label 'process_high'
 
     container "quay.io/nf-core/xeniumranger:4.0"
 
     input:
-    tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform), val(units)
+    tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform), val(units), val(expansion_distance)
 
     output:
     tuple val(meta), path("${prefix}"), emit: outs
@@ -18,7 +18,7 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "XENIUMRANGER_IMPORT_SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+        error "XENIUMRANGER_IMPORTSEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
     prefix = task.ext.prefix ?: "${meta.id}"
@@ -32,6 +32,9 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
 
     def assembled_args = []
     if (task.ext.args) { assembled_args << task.ext.args.trim() }
+    // --expansion-distance is only valid for nuclei-based imports.
+    // xeniumranger rejects it for transcript-assignment imports and cells-only imports.
+    if (nuclei && expansion_distance != null) { assembled_args << "--expansion-distance=${expansion_distance}" }
     if (nuclei) { assembled_args << "--nuclei=\"${nuclei}\"" }
     if (cells) { assembled_args << "--cells=\"${cells}\"" }
     if (transcript_assignment) { assembled_args << "--transcript-assignment=\"${transcript_assignment}\"" }
@@ -48,14 +51,14 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
 
     """
     xeniumranger import-segmentation \\
-        --id="XENIUMRANGER_IMPORT_SEGMENTATION" \\
+        --id="XENIUMRANGER_IMPORTSEGMENTATION" \\
         --xenium-bundle="${xenium_bundle}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         ${args}
 
     rm -rf "${prefix}"
-    mv XENIUMRANGER_IMPORT_SEGMENTATION/outs "${prefix}"
+    mv XENIUMRANGER_IMPORTSEGMENTATION/outs "${prefix}"
     """
 
     stub:

modules/nf-core/xeniumranger/import-segmentation/meta.yml → modules/nf-core/xeniumranger/importsegmentation/meta.yml

@@ -1,6 +1,6 @@
-name: xeniumranger_import_segmentation
+name: XENIUMRANGER_IMPORTSEGMENTATION
 description: |
-  The xeniumranger import-segmentation module runs `xeniumranger import-segmentation`
+  The xeniumranger importsegmentation module runs `xeniumranger import-segmentation`
   to recompute Xenium Onboard Analysis outputs using external segmentation results.
   It supports two execution modes mirroring the Xenium Ranger CLI: an image-based
   mode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together
@@ -102,6 +102,13 @@ input:
         enum:
           - "microns"
           - "pixels"
+    - expansion_distance:
+        type: integer
+        optional: true
+        description: |
+          Distance (in microns) to expand nuclei outward into cell boundaries. Only valid for
+          nuclei-based imports (`nuclei` must be set); xeniumranger rejects it for
+          transcript-assignment imports and cells-only imports. Default: 5. Range: 0-100. 
 output:
   outs:
     - - meta:
@@ -138,4 +145,4 @@ authors:
   - "@dongzehe"
 maintainers:
   - "@khersameesh24"
-  - "@dongzehe"
+  - "@dongzehe"

modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test → modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test

@@ -1,44 +1,46 @@
 nextflow_process {
 
-    name "Test Process XENIUMRANGER_IMPORT_SEGMENTATION"
+    name "Test Process XENIUMRANGER_IMPORTSEGMENTATION"
     script "../main.nf"
-    process "XENIUMRANGER_IMPORT_SEGMENTATION"
+    process "XENIUMRANGER_IMPORTSEGMENTATION"
+    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
     tag "xeniumranger"
-    tag "xeniumranger/import-segmentation"
-    tag "unzip"
+    tag "xeniumranger/importsegmentation"
+    tag "untar"
 
 
     setup {
 
-        run("UNZIP") {
-            script "modules/nf-core/unzip/main.nf"
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
             process {
                 """
-                input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip', checkIfExists: true)]
+                input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe/xenium_bundle.tar.gz', checkIfExists: true)]
                 """
             }
         }
 
     }
 
-    test("xeniumranger import-segmentation nuclei") {
+    test("xeniumranger importsegmentation nuclei") {
         when {
             process {
                 """
-                input[0] = UNZIP.out.unzipped_archive
+                input[0] = UNTAR.out.untar
                     .map { meta, bundle ->
                         [
-                            [id: "test_xeniumranger_import-segmentation"],
+                            [id: "test_xeniumranger_importsegmentation"],
                             bundle,
                             [],
                             [],
                             bundle + "/cells.zarr.zip",
                             [],
                             [],
-                            []
+                            [],
+                            5
                         ]
                     }
                 """
@@ -56,23 +58,24 @@ nextflow_process {
         }
     }
 
-    test("xeniumranger import-segmentation stub") {
+    test("xeniumranger importsegmentation stub") {
         options "-stub"
 
         when {
             process {
                 """
-                input[0] = UNZIP.out.unzipped_archive
+                input[0] = UNTAR.out.untar
                     .map { meta, bundle ->
                         [
-                            [id: "test_xeniumranger_import-segmentation"],
+                            [id: "test_xeniumranger_importsegmentation"],
                             bundle,
                             [],
                             [],
                             bundle + "/cells.zarr.zip",
                             [],
                             [],
-                            []
+                            [],
+                            5
                         ]
                     }
                 """

modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap → modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap

@@ -1,56 +1,56 @@
 {
-    "xeniumranger import-segmentation nuclei": {
+    "xeniumranger importsegmentation stub": {
         "content": [
             {
                 "outs": [
                     [
                         {
-                            "id": "test_xeniumranger_import-segmentation"
+                            "id": "test_xeniumranger_importsegmentation"
                         },
-                        "test_xeniumranger_import-segmentation"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "versions_xeniumranger": [
                     [
-                        "XENIUMRANGER_IMPORT_SEGMENTATION",
+                        "XENIUMRANGER_IMPORTSEGMENTATION",
                         "xeniumranger",
                         "4.0.1.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-06-16T05:59:47.015555128",
+        "timestamp": "2026-07-27T15:02:26.958198169",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.6"
         }
     },
-    "xeniumranger import-segmentation stub": {
+    "xeniumranger importsegmentation nuclei": {
         "content": [
             {
                 "outs": [
                     [
                         {
-                            "id": "test_xeniumranger_import-segmentation"
+                            "id": "test_xeniumranger_importsegmentation"
                         },
-                        [
-                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test_xeniumranger_importsegmentation"
                     ]
                 ],
                 "versions_xeniumranger": [
                     [
-                        "XENIUMRANGER_IMPORT_SEGMENTATION",
+                        "XENIUMRANGER_IMPORTSEGMENTATION",
                         "xeniumranger",
                         "4.0.1.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-06-16T05:59:56.522779629",
+        "timestamp": "2026-07-27T15:02:12.93562615",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.6"
         }
     }
 }

modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config

@@ -0,0 +1,7 @@
+process {
+    withName: XENIUMRANGER_IMPORTSEGMENTATION {
+        cpus   = 2
+        memory = '4.GB'
+        time   = '30.m'
+    }
+}