diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index d45b8ecf..2f6822e4 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -24,7 +24,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
diff --git a/.nf-core.yml b/.nf-core.yml
index c6f8f43c..08a86cf0 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -12,11 +12,13 @@ lint:
 nf_core_version: 3.5.2
 repository_type: pipeline
 template:
-  author: Sameesh Kher, Florian Heyl
+  author: Sameesh Kher, Dongze He, Florian Heyl
   description: A pipeline for spatialomics Xenium In Situ data.
   force: false
   is_nfcore: true
   name: spatialxe
   org: nf-core
   outdir: .
+  skip_features:
+    - igenomes
   version: 1.0.0
diff --git a/README.md b/README.md
index 20285254..6eafaeef 100644
--- a/README.md
+++ b/README.md
@@ -181,11 +181,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use nf-core/spatialxe for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 12d9954f..c1fbf537 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/spatialxe Methods Description"
 section_href: "https://github.com/nf-core/spatialxe"
 plot_type: "html"
-## nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
diff --git a/conf/base.config b/conf/base.config
index 299708cf..e1668aaf 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -14,7 +14,7 @@ process {
     memory = { 6.GB * task.attempt }
     time   = { 4.h  * task.attempt }
 
-    resourceLimits = [ cpus: 192, memory: 750.GB, time: 72.h ]
+    // resourceLimits = [ cpus: 192, memory: 750.GB, time: 72.h ]
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 2147483647) ? 'retry' : 'finish' }
     maxRetries    = 3
@@ -79,7 +79,7 @@ process {
     withLabel:process_gpu {
         ext.use_gpu = { params.use_gpu }
         accelerator = { params.use_gpu ? 1 : null }
-        containerOptions = { "--shm-size ${task.memory.toGiga().intValue()}g" }
+        // containerOptions = { "--shm-size ${task.memory.toGiga().intValue()}g" }
     }
 
     // Single-GPU processes (e.g., Cellpose, StarDist)
diff --git a/conf/modules.config b/conf/modules.config
index 7de4eb2b..22726919 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -218,7 +218,7 @@ process {
 
     withName: PARQUET_TO_CSV {
         publishDir = [
-            path: { "${params.outdir}/${params.mode}/utility/spatialconverter/parquet_to_csv" },
+            path: { "${params.outdir}/${params.mode}/utility/parquet_to_csv" },
             mode: params.publish_dir_mode,
         ]
     }
diff --git a/conf/test_coordinate_mode.config b/conf/test_coordinate_mode.config
index beb99283..e8338a5c 100644
--- a/conf/test_coordinate_mode.config
+++ b/conf/test_coordinate_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile coordinate mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the coordinate mode'
 
     // Input data
diff --git a/conf/test_image_mode.config b/conf/test_image_mode.config
index b9b9665c..17e8124a 100644
--- a/conf/test_image_mode.config
+++ b/conf/test_image_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile image mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the image mode'
 
     // Input data
diff --git a/conf/test_preview_mode.config b/conf/test_preview_mode.config
index 0fa2ce09..144a2349 100644
--- a/conf/test_preview_mode.config
+++ b/conf/test_preview_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile preview mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the preview mode'
 
     // Input data
diff --git a/conf/test_segfree_mode.config b/conf/test_segfree_mode.config
index 72e2a159..5f4467b5 100644
--- a/conf/test_segfree_mode.config
+++ b/conf/test_segfree_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile segfree mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the segfree mode'
 
     // Input data
diff --git a/modules/local/baysor/create_dataset/tests/main.nf.test b/modules/local/baysor/create_dataset/tests/main.nf.test
index 7bd9b6ca..41b2742a 100644
--- a/modules/local/baysor/create_dataset/tests/main.nf.test
+++ b/modules/local/baysor/create_dataset/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file(params.modules_testdata_base_path + "spatial_omics/xenium/homo_sapiens/spatial_gene_expression.csv", checkIfExists: true)
                             ])
@@ -41,7 +41,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file(params.modules_testdata_base_path + "spatial_omics/xenium/homo_sapiens/spatial_gene_expression.csv", checkIfExists: true)
                             ])
diff --git a/modules/local/baysor/preprocess/tests/main.nf.test b/modules/local/baysor/preprocess/tests/main.nf.test
index 122fbdde..f3112c25 100644
--- a/modules/local/baysor/preprocess/tests/main.nf.test
+++ b/modules/local/baysor/preprocess/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true)
                             ])
@@ -45,7 +45,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true)
                             ])
diff --git a/modules/local/baysor/preview/tests/main.nf.test b/modules/local/baysor/preview/tests/main.nf.test
index c4fbde32..d3f522d7 100644
--- a/modules/local/baysor/preview/tests/main.nf.test
+++ b/modules/local/baysor/preview/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)
@@ -41,7 +41,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)
diff --git a/modules/local/baysor/run/tests/main.nf.test b/modules/local/baysor/run/tests/main.nf.test
index 2ae31336..37cda127 100644
--- a/modules/local/baysor/run/tests/main.nf.test
+++ b/modules/local/baysor/run/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 [],
@@ -46,7 +46,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 [],
diff --git a/modules/local/baysor/segfree/tests/main.nf.test b/modules/local/baysor/segfree/tests/main.nf.test
index d7e8ce12..1fb7d2bc 100644
--- a/modules/local/baysor/segfree/tests/main.nf.test
+++ b/modules/local/baysor/segfree/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)
@@ -41,7 +41,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)
diff --git a/modules/local/ficture/model/main.nf b/modules/local/ficture/model/main.nf
index 4eea675b..34c2dbc0 100644
--- a/modules/local/ficture/model/main.nf
+++ b/modules/local/ficture/model/main.nf
@@ -20,7 +20,6 @@ process FICTURE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     def features_list = features ? "--in-feature ${features}": ""
 
     """
@@ -33,12 +32,11 @@ process FICTURE {
         --n-factor 6,12 \\
         --n-jobs ${task.cpus} \\
         --plot-each-factor \\
-        --all
+        --all \\
+        ${args}
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p results/
     """
diff --git a/modules/local/ficture/preprocess/main.nf b/modules/local/ficture/preprocess/main.nf
index c412b1b9..7ec3c081 100644
--- a/modules/local/ficture/preprocess/main.nf
+++ b/modules/local/ficture/preprocess/main.nf
@@ -27,7 +27,8 @@ process FICTURE_PREPROCESS {
     ficture_preprocess.py \\
         --transcripts ${transcripts} \\
         ${features_arg} \\
-        --negative-control-regex '${params.negative_control_regex}'
+        --negative-control-regex '${params.negative_control_regex}' \\
+        ${args}
     """
 
     stub:
diff --git a/modules/local/proseg/proseg2baysor/tests/main.nf.test b/modules/local/proseg/proseg2baysor/tests/main.nf.test
index fe8a8031..039217e0 100644
--- a/modules/local/proseg/proseg2baysor/tests/main.nf.test
+++ b/modules/local/proseg/proseg2baysor/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                             [id: "test_run_proseg2baysor"],
                         ]).combine(PROSEG.out.seg_outs, by: 0)
                 """
@@ -53,7 +53,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                             [id: "test_run_proseg2baysor"],
                         ]).combine(PROSEG.out.seg_outs, by: 0)
                 """
diff --git a/modules/local/resolift/tests/tags.yml b/modules/local/resolift/tests/tags.yml
deleted file mode 100644
index 93ee19d3..00000000
--- a/modules/local/resolift/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-resolift:
-  - "modules/local/resolift/**"
diff --git a/modules/local/utility/convert_mask_uint32/main.nf b/modules/local/utility/convert_mask_uint32/main.nf
index 9102b183..fd2a3bff 100644
--- a/modules/local/utility/convert_mask_uint32/main.nf
+++ b/modules/local/utility/convert_mask_uint32/main.nf
@@ -16,7 +16,6 @@ process CONVERT_MASK_UINT32 {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.12 conda-forge::tifffile conda-forge::numpy"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d964e0bef867bb2ff1a309c9c087d8d83ac734ce3aa315dd8311d4c1bfdafd8e/data' :
         'community.wave.seqera.io/library/python_pip_imagecodecs_nvidia-cublas-cu12_pruned:b668bcb6d531d350' }"
diff --git a/modules/local/utility/extract_dapi/main.nf b/modules/local/utility/extract_dapi/main.nf
index 791a8a92..adbc6d87 100644
--- a/modules/local/utility/extract_dapi/main.nf
+++ b/modules/local/utility/extract_dapi/main.nf
@@ -16,7 +16,6 @@ process EXTRACT_DAPI {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.12 conda-forge::tifffile conda-forge::numpy"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d964e0bef867bb2ff1a309c9c087d8d83ac734ce3aa315dd8311d4c1bfdafd8e/data' :
         'community.wave.seqera.io/library/python_pip_imagecodecs_nvidia-cublas-cu12_pruned:b668bcb6d531d350' }"
diff --git a/modules/local/utility/spatialconverter/parquet_to_csv/main.nf b/modules/local/utility/parquet_to_csv/main.nf
similarity index 100%
rename from modules/local/utility/spatialconverter/parquet_to_csv/main.nf
rename to modules/local/utility/parquet_to_csv/main.nf
diff --git a/modules/local/utility/spatialconverter/parquet_to_csv/meta.yml b/modules/local/utility/parquet_to_csv/meta.yml
similarity index 94%
rename from modules/local/utility/spatialconverter/parquet_to_csv/meta.yml
rename to modules/local/utility/parquet_to_csv/meta.yml
index 0d7a8611..60d58fcc 100644
--- a/modules/local/utility/spatialconverter/parquet_to_csv/meta.yml
+++ b/modules/local/utility/parquet_to_csv/meta.yml
@@ -1,9 +1,9 @@
-name: "spatialconverter_parquet_to_csv"
+name: "parquet_to_csv"
 description: Tool suite for spatial omics data conversions.
 keywords:
   - xenium
 tools:
-  - "spatialconverter":
+  - "parquet_to_csv":
       description: "Collects functions to convert data formats for various types of data processing and analysis for spatial omics data."
       homepage: "https://github.com/heylf/spatialconverter"
       documentation: "https://github.com/heylf/spatialconverter"
diff --git a/modules/local/utility/spatialconverter/parquet_to_csv/resources/usr/bin/parquet_to_csv.py b/modules/local/utility/parquet_to_csv/resources/usr/bin/parquet_to_csv.py
similarity index 100%
rename from modules/local/utility/spatialconverter/parquet_to_csv/resources/usr/bin/parquet_to_csv.py
rename to modules/local/utility/parquet_to_csv/resources/usr/bin/parquet_to_csv.py
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
index 54d3ba00..e61cdc11 100644
--- a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_import-segmentation"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = 0
@@ -93,7 +93,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_import-segmentation"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = 0
@@ -159,7 +159,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_import-segmentation"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = 0
@@ -225,7 +225,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_import-segmentation"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = 0
@@ -292,7 +292,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_import-segmentation"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = 0
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
index d0962738..7c37a32a 100644
--- a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_relabel"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
@@ -76,7 +76,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_relabel"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
index 861c2414..36f26f46 100644
--- a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_resegment"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = []
@@ -57,7 +57,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                         [id: "test_xeniumranger_resegment"],
                     ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
                 input[1] = []
diff --git a/nextflow.config b/nextflow.config
index bc551340..73be717e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -130,7 +130,6 @@ params {
     restrict_concurrency       = false       // restrict running certain process in parallel
 
     // Boilerplate options
-    outdir                       = null
     publish_dir_mode             = 'copy'
     email                        = null
     email_on_fail                = null
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index ef0b01d9..89f81f6a 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
             "datePublished": "2026-04-28T15:09:48+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/spatialxe)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/spatialxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/spatialxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium data. The current plan for the pipeline implementation is shown in the metromap below. **The pipeline is under active developement and changes might occure frequently**.\n\n![nf-core/spatialxe-metromap](docs/images/spatialxe-metromap.png)\n\n> [!NOTE]\n> We are currently testing the pipeline for the [10x Atera system](https://www.10xgenomics.com/platforms/atera).\n\n## Tools supported\n\nThe pipeline supports the following tools:\n\n- Segmenation methods:\n  - [Baysor](https://doi.org/10.1038/s41587-021-01044-w)\n  - [Cellpose](https://doi.org/10.1038/s41592-020-01018-x)\n  - [Xenium ranger (XR)](https://www.10xgenomics.com/support/software/xenium-ranger/latest)\n  - [StarDist](https://doi.org/10.48550/arXiv.2203.02284)\n- Segmentation free methods:\n  - [Ficture](https://doi.org/10.1038/s41592-024-02415-2)\n  - [Baysor](https://doi.org/10.1038/s41587-021-01044-w)\n- Transcript assignment methods:\n  - [Segger](https://doi.org/10.1101/2025.03.14.643160)\n  - [Proseg](https://doi.org/10.1038/s41592-025-02697-0)\n- Utility methods:\n  - [SpatialData](https://doi.org/10.1038/s41592-024-02212-x)\n  - [Baysor](https://doi.org/10.1038/s41587-021-01044-w)\n- QC methods:\n  - [MultiQC Xenium Extra Plugin](https://github.com/MultiQC/xenium-extra)\n  - [OPT](https://github.com/JEFworks-Lab/off-target-probe-tracker)\n\n## Usage\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/spatialxe/results).\n\n> [!NOTE]\n> The pipeline does not support conda currently. We are working on it.\n\n## Quick Start\n\n`samplesheet.csv`:\n\n```csv\nsample,bundle,image\ntest_sample,/path/to/xenium-bundle,/path/to/morphology.ome.tif\n```\n\nNow, you can run the pipeline using:\n\n### Run image-based segmentation mode <br>\n\n`CELLPOSE -> BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode <MODE>\n```\n\n### Run coordinate-based segmentation mode <br>\n\n`PROSEG -> PROSEG2BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode coordinate\n```\n\n### Run segfree mode <br>\n\n`BAYSOR_SEGFREE`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode segfree\n```\n\n### Run preview mode <br>\n\n`BAYSOR_PREVIEW`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode preview\n```\n\n### Run just the quality control <br>\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode qc\n```\n\n### Additional information\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/spatialxe/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/spatialxe/output).\n\n## Runtime and resource estimations\n\n| Tool                      | Compute | Runtime (min / med / max) | Peak RSS (min / med / max) |\n| ------------------------- | ------- | ------------------------- | -------------------------- |\n| Cellpose                  | GPU     | 1m / 4m / 1.4h            | 10 GB / 26 GB / 554 GB     |\n| Cellpose                  | CPU     | 1.3h / 2.3h / 6.5h        | 161 GB / 426 GB / 1115 GB  |\n| StarDist                  | GPU     | 1m / 4m / 7m              | 5 GB / 12 GB / 18 GB       |\n| StarDist                  | CPU     | 5m / 6m / 7m              | 18 GB / 18 GB / 18 GB      |\n| Segger (create_dataset)   | GPU     | 2m / 9m / 31m             | 1.7 GB / 14 GB / 50 GB     |\n| Segger (create_dataset)   | CPU     | 13m / 21m / 46m           | 13 GB / 19 GB / 49 GB      |\n| Segger (train)            | GPU     | 10m / 43m / 2.9h          | 30 GB / 33 GB / 60 GB      |\n| Segger (predict)          | GPU     | 2m / 16m / 59m            | 10 GB / 25 GB / 87 GB      |\n| Baysor (whole-image)      | CPU     | 2m / 30m / 17h            | 6 GB / 10 GB / 650 GB      |\n| Baysor (tiled)            | CPU     | 1m / 18m / 13h            | 0.2 GB / 34 GB / 530 GB    |\n| Proseg                    | CPU     | 1m / 18m / 6.8h           | 279 MB / 3.8 GB / 136 GB   |\n| XeniumRanger (resegment)  | CPU     | 18m / 39m / 3.7h          | 28 GB / 54 GB / 60 GB      |\n| XeniumRanger (import_seg) | CPU     | 2m / 7m / 2.7h            | 2.6 GB / 11 GB / 51 GB     |\n| Ficture (preprocess)      | CPU     | 3m / 4m / 13m             | 331 MB / 357 MB / 21 GB    |\n\n- Cellpose GPU vs CPU: 35x faster on GPU (4m median vs 2.3h), 16x less memory (26 GB vs 426 GB)\n- Segger: Only tool that truly requires GPU for all 3 steps (create_dataset, train, predict)\n- StarDist: Very fast on CPU, GPU is not necessary to run its default model\n\n## Credits\n\nnf-core/spatialxe is mainly developed by [Sameesh Kher](https://github.com/khersameesh24), [Dongze He](https://github.com/dongzehe), and [Florian Heyl](https://github.com/heylf).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Tobias Krause\n- Kre\u0161imir Be\u0161tak (kbestak)\n- Matthias H\u00f6rtenhuber (mashehu)\n- Maxime Garcia (maxulysse)\n- K\u00fcbra Narc\u0131 (kubranarci)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/spatialxe for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/spatialxe)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/spatialxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/spatialxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium data. The current plan for the pipeline implementation is shown in the metromap below. **The pipeline is under active developement and changes might occure frequently**.\n\n![nf-core/spatialxe-metromap](docs/images/spatialxe-metromap.png)\n\n> [!NOTE]\n> We are currently testing the pipeline for the [10x Atera system](https://www.10xgenomics.com/platforms/atera).\n\n## Tools supported\n\nThe pipeline supports the following tools:\n\n- Segmenation methods:\n  - [Baysor](https://doi.org/10.1038/s41587-021-01044-w)\n  - [Cellpose](https://doi.org/10.1038/s41592-020-01018-x)\n  - [Xenium ranger (XR)](https://www.10xgenomics.com/support/software/xenium-ranger/latest)\n  - [StarDist](https://doi.org/10.48550/arXiv.2203.02284)\n- Segmentation free methods:\n  - [Ficture](https://doi.org/10.1038/s41592-024-02415-2)\n  - [Baysor](https://doi.org/10.1038/s41587-021-01044-w)\n- Transcript assignment methods:\n  - [Segger](https://doi.org/10.1101/2025.03.14.643160)\n  - [Proseg](https://doi.org/10.1038/s41592-025-02697-0)\n- Utility methods:\n  - [SpatialData](https://doi.org/10.1038/s41592-024-02212-x)\n  - [Baysor](https://doi.org/10.1038/s41587-021-01044-w)\n- QC methods:\n  - [MultiQC Xenium Extra Plugin](https://github.com/MultiQC/xenium-extra)\n  - [OPT](https://github.com/JEFworks-Lab/off-target-probe-tracker)\n\n## Usage\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/spatialxe/results).\n\n> [!NOTE]\n> The pipeline does not support conda currently. We are working on it.\n\n## Quick Start\n\n`samplesheet.csv`:\n\n```csv\nsample,bundle,image\ntest_sample,/path/to/xenium-bundle,/path/to/morphology.ome.tif\n```\n\nNow, you can run the pipeline using:\n\n### Run image-based segmentation mode <br>\n\n`CELLPOSE -> BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode <MODE>\n```\n\n### Run coordinate-based segmentation mode <br>\n\n`PROSEG -> PROSEG2BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode coordinate\n```\n\n### Run segfree mode <br>\n\n`BAYSOR_SEGFREE`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode segfree\n```\n\n### Run preview mode <br>\n\n`BAYSOR_PREVIEW`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode preview\n```\n\n### Run just the quality control <br>\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode qc\n```\n\n### Additional information\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/spatialxe/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/spatialxe/output).\n\n## Runtime and resource estimations\n\n| Tool                      | Compute | Runtime (min / med / max) | Peak RSS (min / med / max) |\n| ------------------------- | ------- | ------------------------- | -------------------------- |\n| Cellpose                  | GPU     | 1m / 4m / 1.4h            | 10 GB / 26 GB / 554 GB     |\n| Cellpose                  | CPU     | 1.3h / 2.3h / 6.5h        | 161 GB / 426 GB / 1115 GB  |\n| StarDist                  | GPU     | 1m / 4m / 7m              | 5 GB / 12 GB / 18 GB       |\n| StarDist                  | CPU     | 5m / 6m / 7m              | 18 GB / 18 GB / 18 GB      |\n| Segger (create_dataset)   | GPU     | 2m / 9m / 31m             | 1.7 GB / 14 GB / 50 GB     |\n| Segger (create_dataset)   | CPU     | 13m / 21m / 46m           | 13 GB / 19 GB / 49 GB      |\n| Segger (train)            | GPU     | 10m / 43m / 2.9h          | 30 GB / 33 GB / 60 GB      |\n| Segger (predict)          | GPU     | 2m / 16m / 59m            | 10 GB / 25 GB / 87 GB      |\n| Baysor (whole-image)      | CPU     | 2m / 30m / 17h            | 6 GB / 10 GB / 650 GB      |\n| Baysor (tiled)            | CPU     | 1m / 18m / 13h            | 0.2 GB / 34 GB / 530 GB    |\n| Proseg                    | CPU     | 1m / 18m / 6.8h           | 279 MB / 3.8 GB / 136 GB   |\n| XeniumRanger (resegment)  | CPU     | 18m / 39m / 3.7h          | 28 GB / 54 GB / 60 GB      |\n| XeniumRanger (import_seg) | CPU     | 2m / 7m / 2.7h            | 2.6 GB / 11 GB / 51 GB     |\n| Ficture (preprocess)      | CPU     | 3m / 4m / 13m             | 331 MB / 357 MB / 21 GB    |\n\n- Cellpose GPU vs CPU: 35x faster on GPU (4m median vs 2.3h), 16x less memory (26 GB vs 426 GB)\n- Segger: Only tool that truly requires GPU for all 3 steps (create_dataset, train, predict)\n- StarDist: Very fast on CPU, GPU is not necessary to run its default model\n\n## Credits\n\nnf-core/spatialxe is mainly developed by [Sameesh Kher](https://github.com/khersameesh24), [Dongze He](https://github.com/dongzehe), and [Florian Heyl](https://github.com/heylf).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Tobias Krause\n- Kre\u0161imir Be\u0161tak (kbestak)\n- Matthias H\u00f6rtenhuber (mashehu)\n- Maxime Garcia (maxulysse)\n- K\u00fcbra Narc\u0131 (kubranarci)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- If you use nf-core/spatialxe for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
diff --git a/subworkflows/local/baysor_generate_preview/main.nf b/subworkflows/local/baysor_generate_preview/main.nf
index 3c4112c1..2494fcbd 100644
--- a/subworkflows/local/baysor_generate_preview/main.nf
+++ b/subworkflows/local/baysor_generate_preview/main.nf
@@ -5,7 +5,7 @@
 include { BAYSOR_PREVIEW        } from '../../../modules/local/baysor/preview/main'
 include { BAYSOR_CREATE_DATASET } from '../../../modules/local/baysor/create_dataset/main'
 include { EXTRACT_PREVIEW_DATA  } from '../../../modules/local/utility/extract_preview_data/main'
-include { PARQUET_TO_CSV        } from '../../../modules/local/utility/spatialconverter/parquet_to_csv/main'
+include { PARQUET_TO_CSV        } from '../../../modules/local/utility/parquet_to_csv/main'
 
 workflow BAYSOR_GENERATE_PREVIEW {
     take:
@@ -14,9 +14,8 @@ workflow BAYSOR_GENERATE_PREVIEW {
 
     main:
 
-    ch_versions         = Channel.empty()
-    ch_preview_mqc_html = Channel.empty()
-    ch_preview_mqc_png  = Channel.empty()
+    ch_preview_mqc_html = channel.empty()
+    ch_preview_mqc_png  = channel.empty()
 
 
     // run parquet to csv
@@ -47,5 +46,4 @@ workflow BAYSOR_GENERATE_PREVIEW {
     emit:
     preview_html = ch_preview_mqc_html // channel: [ val(meta), ["*_mqc.tsv"] ]
     preview_img  = ch_preview_mqc_png  // channel: [ val(meta), ["*_mqc.png"] ]
-    versions     = ch_versions         // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/baysor_generate_segfree/main.nf b/subworkflows/local/baysor_generate_segfree/main.nf
index 02ff44c8..52e2e699 100644
--- a/subworkflows/local/baysor_generate_segfree/main.nf
+++ b/subworkflows/local/baysor_generate_segfree/main.nf
@@ -13,9 +13,7 @@ workflow BAYSOR_GENERATE_SEGFREE {
 
     main:
 
-    ch_versions = Channel.empty()
-
-    ch_transcripts = Channel.empty()
+    ch_transcripts = channel.empty()
 
     // Always preprocess transcripts.parquet to CSV for Baysor 0.7.1 compatibility.
     // Baysor's Julia Parquet.jl cannot read zstd-compressed parquet files from Xenium bundles.
@@ -43,7 +41,7 @@ workflow BAYSOR_GENERATE_SEGFREE {
     BAYSOR_SEGFREE(
         ch_baysor_segfree_input
     )
+
     emit:
     ncvs     = BAYSOR_SEGFREE.out.ncvs // channel: [ val(meta), ["ncvs.loom"] ]
-    versions = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/baysor_run_prior_segmentation_mask/main.nf b/subworkflows/local/baysor_run_prior_segmentation_mask/main.nf
index 02eaaec8..17025571 100644
--- a/subworkflows/local/baysor_run_prior_segmentation_mask/main.nf
+++ b/subworkflows/local/baysor_run_prior_segmentation_mask/main.nf
@@ -16,12 +16,10 @@ workflow BAYSOR_RUN_PRIOR_SEGMENTATION_MASK {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_transcripts = channel.empty()
 
-    ch_transcripts = Channel.empty()
-
-    ch_redefined_bundle = Channel.empty()
-    ch_coordinate_space = Channel.value("pixels")
+    ch_redefined_bundle = channel.empty()
+    ch_coordinate_space = channel.value("pixels")
 
     // Always preprocess transcripts.parquet to CSV for Baysor 0.7.1 compatibility.
     // Baysor's Julia Parquet.jl cannot read zstd-compressed parquet files from Xenium bundles.
@@ -77,5 +75,4 @@ workflow BAYSOR_RUN_PRIOR_SEGMENTATION_MASK {
     emit:
     coordinate_space = ch_coordinate_space // channel: [ "pixels" ]
     redefined_bundle = ch_redefined_bundle // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions         = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/baysor_run_transcripts_parquet/main.nf b/subworkflows/local/baysor_run_transcripts_parquet/main.nf
index c085a34f..26f9283b 100644
--- a/subworkflows/local/baysor_run_transcripts_parquet/main.nf
+++ b/subworkflows/local/baysor_run_transcripts_parquet/main.nf
@@ -29,8 +29,7 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_coordinate_space = Channel.value("microns")
+    ch_coordinate_space = channel.value("microns")
 
     if ( params.baysor_tiling ) {
 
@@ -155,5 +154,4 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET {
     emit:
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs
     coordinate_space = ch_coordinate_space
-    versions         = ch_versions
 }
diff --git a/subworkflows/local/baysor_run_transcripts_parquet_tiled/main.nf b/subworkflows/local/baysor_run_transcripts_parquet_tiled/main.nf
index 23435886..16cb06dd 100644
--- a/subworkflows/local/baysor_run_transcripts_parquet_tiled/main.nf
+++ b/subworkflows/local/baysor_run_transcripts_parquet_tiled/main.nf
@@ -17,7 +17,7 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET_TILED {
 
     main:
 
-    ch_coordinate_space = Channel.value("microns")
+    ch_coordinate_space = channel.value("microns")
 
     // Step 1: Divide transcripts into overlapping patches
     XENIUM_PATCH_DIVIDE ( ch_transcripts_file )
diff --git a/subworkflows/local/cellpose_baysor_import_segmentation/main.nf b/subworkflows/local/cellpose_baysor_import_segmentation/main.nf
index 9f89162f..011d9477 100644
--- a/subworkflows/local/cellpose_baysor_import_segmentation/main.nf
+++ b/subworkflows/local/cellpose_baysor_import_segmentation/main.nf
@@ -23,11 +23,9 @@ workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_transcripts = Channel.empty()
-    ch_imp_seg_inputs = Channel.empty()
-    ch_filtered_transcripts = Channel.empty()
-    ch_coordinate_space = Channel.value("microns")
+    ch_transcripts = channel.empty()
+    ch_imp_seg_inputs = channel.empty()
+    ch_coordinate_space = channel.value("microns")
 
 
     // Use empty list when no model is provided; path input for official cellpose module
@@ -180,5 +178,4 @@ workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
     emit:
     coordinate_space = ch_coordinate_space                         // channel: [ val("microns") ]
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions = ch_versions                                         // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf b/subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf
index 2fda9ec2..bc81a5d7 100644
--- a/subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf
+++ b/subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf
@@ -18,9 +18,8 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_imp_seg_inputs = Channel.empty()
-    ch_coordinate_space = Channel.value("pixels")
+    ch_imp_seg_inputs = channel.empty()
+    ch_coordinate_space = channel.value("pixels")
 
     // Use empty list when no model is provided; path input for official cellpose module
     cellpose_model = params.cellpose_model ? file(params.cellpose_model) : []
@@ -50,7 +49,7 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
     else {
 
         ch_cellpose_input = ch_image
-        ch_scale_info = Channel.empty()
+        ch_scale_info = channel.empty()
     }
 
     // run cellpose on morphology tiff (or downscaled version)
@@ -134,5 +133,4 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
     emit:
     coordinate_space = ch_coordinate_space // channel: [ ["pixels"] ]
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions         = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/ficture_preprocess_model/main.nf b/subworkflows/local/ficture_preprocess_model/main.nf
index 203d057e..06d4edf2 100644
--- a/subworkflows/local/ficture_preprocess_model/main.nf
+++ b/subworkflows/local/ficture_preprocess_model/main.nf
@@ -4,7 +4,7 @@
 
 include { FICTURE_PREPROCESS } from '../../../modules/local/ficture/preprocess/main'
 include { FICTURE            } from '../../../modules/local/ficture/model/main'
-include { PARQUET_TO_CSV     } from '../../../modules/local/utility/spatialconverter/parquet_to_csv/main'
+include { PARQUET_TO_CSV     } from '../../../modules/local/utility/parquet_to_csv/main'
 
 
 
@@ -15,8 +15,6 @@ workflow FICTURE_PREPROCESS_MODEL {
 
     main:
 
-    ch_versions = Channel.empty()
-
     // convert parquet to csv
     PARQUET_TO_CSV(ch_transcripts_file, ".csv")
 
@@ -26,7 +24,7 @@ workflow FICTURE_PREPROCESS_MODEL {
     FICTURE_PREPROCESS(ch_transcripts, ch_features)
 
     // run the ficture wrapper pipeline
-    ch_features_clean = params.features ? FICTURE_PREPROCESS.out.features : Channel.value([])
+    ch_features_clean = params.features ? FICTURE_PREPROCESS.out.features : channel.value([])
     FICTURE(
         FICTURE_PREPROCESS.out.transcripts,
         FICTURE_PREPROCESS.out.coordinate_minmax,
@@ -37,5 +35,4 @@ workflow FICTURE_PREPROCESS_MODEL {
     coordinate_minmax = FICTURE_PREPROCESS.out.coordinate_minmax // channel: [ "*coordinate_minmax.tsv" ]
     features          = FICTURE_PREPROCESS.out.features // channel: [ "*feature.clean.tsv.gz" ]
     results           = FICTURE.out.results // channel: [ val(meta), [ "results/** ] ]
-    versions          = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/opt_flip_track_stat/main.nf b/subworkflows/local/opt_flip_track_stat/main.nf
index 916268ad..839768d2 100644
--- a/subworkflows/local/opt_flip_track_stat/main.nf
+++ b/subworkflows/local/opt_flip_track_stat/main.nf
@@ -11,8 +11,8 @@ workflow OPT_FLIP_TRACK_STAT {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_summary = Channel.empty()
+    ch_versions = channel.empty()
+    ch_summary = channel.empty()
 
     // correct probes that are aligning to opposite strand with `flip`
     OPT_FLIP(ch_probe_fasta, ch_references)
diff --git a/subworkflows/local/proseg_preset_proseg2baysor/main.nf b/subworkflows/local/proseg_preset_proseg2baysor/main.nf
index 757e319f..3f9d8c99 100644
--- a/subworkflows/local/proseg_preset_proseg2baysor/main.nf
+++ b/subworkflows/local/proseg_preset_proseg2baysor/main.nf
@@ -13,8 +13,7 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_coordinate_space = Channel.value("microns")
+    ch_coordinate_space = channel.value("microns")
 
     // run proseg with the xenium format
     PROSEG(ch_transcripts_file)
@@ -48,5 +47,4 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR {
     emit:
     coordinate_space = ch_coordinate_space // channel: [ "microns" ]
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions         = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/proseg_preset_proseg2baysor_tiled/main.nf b/subworkflows/local/proseg_preset_proseg2baysor_tiled/main.nf
index ab141ae8..afeca1a0 100644
--- a/subworkflows/local/proseg_preset_proseg2baysor_tiled/main.nf
+++ b/subworkflows/local/proseg_preset_proseg2baysor_tiled/main.nf
@@ -16,8 +16,7 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR_TILED {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_coordinate_space = Channel.value("microns")
+    ch_coordinate_space = channel.value("microns")
 
     // Step 1: Divide transcripts into overlapping patches
     XENIUM_PATCH_DIVIDE ( ch_transcripts_file )
@@ -84,5 +83,4 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR_TILED {
     emit:
     coordinate_space = ch_coordinate_space                          // channel: [ "microns" ]
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs    // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions         = ch_versions                                  // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/segger_create_train_predict/main.nf b/subworkflows/local/segger_create_train_predict/main.nf
index 97c38aad..7e3b8b74 100644
--- a/subworkflows/local/segger_create_train_predict/main.nf
+++ b/subworkflows/local/segger_create_train_predict/main.nf
@@ -15,10 +15,9 @@ workflow SEGGER_CREATE_TRAIN_PREDICT {
 
     main:
 
-    ch_versions = Channel.empty()
     // Note: spatialxe uses "pixels" but per 10x docs, transcript-based segmentation
     // (like Baysor/Segger) must use "microns" since Xenium coordinates are in microns
-    ch_coordinate_space = Channel.value("microns")
+    ch_coordinate_space = channel.value("microns")
 
     // create dataset (always needed for predict step)
     SEGGER_CREATE_DATASET(ch_bundle)
@@ -74,5 +73,4 @@ workflow SEGGER_CREATE_TRAIN_PREDICT {
     emit:
     coordinate_space = ch_coordinate_space // channel: [ "microns" ]
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions         = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/spatialdata_write_meta_merge/main.nf b/subworkflows/local/spatialdata_write_meta_merge/main.nf
index 68ddf26c..32052d85 100644
--- a/subworkflows/local/spatialdata_write_meta_merge/main.nf
+++ b/subworkflows/local/spatialdata_write_meta_merge/main.nf
@@ -15,29 +15,28 @@ workflow SPATIALDATA_WRITE_META_MERGE {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_segmented_object = Channel.empty()
+    ch_segmented_object = channel.empty()
 
     // check segmentation - only nuclei, cells or both cells & nuclei
     if (params.mode == 'image') {
 
         if (params.nucleus_segmentation_only && params.cell_segmentation_only) {
-            ch_segmented_object = Channel.value('cells_and_nuclei')
+            ch_segmented_object = channel.value('cells_and_nuclei')
         }
         else if (params.nucleus_segmentation_only) {
-            ch_segmented_object = Channel.value('nuclei')
+            ch_segmented_object = channel.value('nuclei')
         }
         else if (params.cell_segmentation_only) {
-            ch_segmented_object = Channel.value('cells')
+            ch_segmented_object = channel.value('cells')
         }
         else {
-            ch_segmented_object = Channel.value([])
+            ch_segmented_object = channel.value([])
         }
     }
 
     // set all boundaries as false - default
     if (params.mode == 'coordinate') {
-        ch_segmented_object = Channel.value([])
+        ch_segmented_object = channel.value([])
     }
 
     // write spatialdata object from the raw xenium bundle
@@ -76,5 +75,4 @@ workflow SPATIALDATA_WRITE_META_MERGE {
     sd_redefined_bundle = SPATIALDATA_WRITE_REDEFINED_BUNDLE.out.spatialdata // channel: [ val(meta), "spatialdata_redefined" ]
     sd_merged_bundle    = SPATIALDATA_MERGE_RAW_REDEFINED.out.merged_bundle // channel: [ val(meta), "spatialdata_merged" ]
     sd_metadata         = SPATIALDATA_META.out.metadata // channel: [ val(meta), "spatialdata_meta" ]
-    versions            = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/stardist_resolift_morphology_ome_tif/main.nf b/subworkflows/local/stardist_resolift_morphology_ome_tif/main.nf
index ad338f57..ad2188c2 100644
--- a/subworkflows/local/stardist_resolift_morphology_ome_tif/main.nf
+++ b/subworkflows/local/stardist_resolift_morphology_ome_tif/main.nf
@@ -15,9 +15,8 @@ workflow STARDIST_RESOLIFT_MORPHOLOGY_OME_TIF {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_imp_seg_inputs = Channel.empty()
-    ch_coordinate_space = Channel.value("pixels")
+    ch_imp_seg_inputs = channel.empty()
+    ch_coordinate_space = channel.value("pixels")
 
     // Use default model when no model is provided
     stardist_nuclei_model = params.stardist_nuclei_model ?: '2D_versatile_fluo'
@@ -66,5 +65,4 @@ workflow STARDIST_RESOLIFT_MORPHOLOGY_OME_TIF {
     emit:
     coordinate_space = ch_coordinate_space // channel: [ ["pixels"] ]
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs // channel: [ val(meta), ["redefined-xenium-bundle"] ]
-    versions         = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf b/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
index 51bf77b2..b812e1c7 100644
--- a/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
@@ -37,8 +37,6 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
-
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
@@ -101,7 +99,7 @@ workflow PIPELINE_INITIALISATION {
     //
     try {
 
-        Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
+        channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
             .map { meta, bundle, image ->
                 return [[id: meta.id], bundle, image]
             }
@@ -125,7 +123,6 @@ workflow PIPELINE_INITIALISATION {
 
     emit:
     samplesheet = ch_samplesheet
-    versions    = ch_versions
 }
 
 /*
@@ -331,7 +328,6 @@ def validateXeniumBundle(ch_samplesheet) {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
-    // TODO nf-core: Optionally add in-text citation tools to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
@@ -344,7 +340,6 @@ def toolCitationText() {
 }
 
 def toolBibliographyText() {
-    // TODO nf-core: Optionally add bibliographic entries to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
@@ -381,11 +376,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["tool_citations"] = ""
     meta["tool_bibliography"] = ""
 
-    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+    // Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
     // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
     // meta["tool_bibliography"] = toolBibliographyText()
 
-
     def methods_text = mqc_methods_yaml.text
 
     def engine = new groovy.text.SimpleTemplateEngine()
diff --git a/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf b/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
index 4940e6d3..e18b36ec 100644
--- a/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
+++ b/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
@@ -13,9 +13,9 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_redefined_bundle = Channel.empty()
-    ch_coordinate_space = Channel.empty()
+    ch_versions = channel.empty()
+    ch_redefined_bundle = channel.empty()
+    ch_coordinate_space = channel.empty()
 
     cells = ch_bundle_path.map { meta, bundle ->
         return [meta, bundle + "/cells.zarr.zip"]
diff --git a/subworkflows/local/xeniumranger_relabel_resegment/main.nf b/subworkflows/local/xeniumranger_relabel_resegment/main.nf
index 8dc95d6f..424224a7 100644
--- a/subworkflows/local/xeniumranger_relabel_resegment/main.nf
+++ b/subworkflows/local/xeniumranger_relabel_resegment/main.nf
@@ -12,7 +12,7 @@ workflow XENIUMRANGER_RELABEL_RESEGMENT {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     // Combine bundle path with gene panel into a single tuple for relabel
     XENIUMRANGER_RELABEL(
diff --git a/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf b/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
index 6de384e3..fce90bb6 100644
--- a/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
+++ b/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
@@ -11,9 +11,8 @@ workflow XENIUMRANGER_RESEGMENT_MORPHOLOGY_OME_TIF {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_redefined_bundle = Channel.empty()
-    ch_coordinate_space = Channel.value("pixels")
+    ch_redefined_bundle = channel.empty()
+    ch_coordinate_space = channel.value("pixels")
 
     // run resegment with changed config values
     XENIUMRANGER_RESEGMENT(ch_bundle_path)
@@ -58,5 +57,4 @@ workflow XENIUMRANGER_RESEGMENT_MORPHOLOGY_OME_TIF {
     emit:
     redefined_bundle = ch_redefined_bundle // channel: [ val(meta), ["redefined-xenium-bundle"] ]
     coordinate_space = ch_coordinate_space // channel: [ ["pixels"] ]
-    versions         = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
index 68718e4f..897d6681 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -40,9 +40,9 @@ nextflow_function {
         }
     }
 
-    test("Test Function checkCondaChannels") {
+    test("Test Function checkCondachannels") {
 
-        function "checkCondaChannels"
+        function "checkCondachannels"
 
         then {
             assertAll(
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
index e3f0baf4..f03a352a 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -9,7 +9,7 @@
         },
         "timestamp": "2024-02-28T12:02:05.308243"
     },
-    "Test Function checkCondaChannels": {
+    "Test Function checkCondachannels": {
         "content": null,
         "meta": {
             "nf-test": "0.8.4",
diff --git a/tests/coordinate_mode.nf.test b/tests/coordinate_mode.nf.test
index b6240f32..51623327 100644
--- a/tests/coordinate_mode.nf.test
+++ b/tests/coordinate_mode.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     config "../conf/test_coordinate_mode.config"
 
-    test("-profile test") {
+    test("-profile test stub") {
 
         options "-stub"
 
diff --git a/tests/coordinate_mode.nf.test.snap b/tests/coordinate_mode.nf.test.snap
index 6e10be9d..828fe335 100644
--- a/tests/coordinate_mode.nf.test.snap
+++ b/tests/coordinate_mode.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "-profile test": {
+    "-profile test stub": {
         "content": [
             {
                 "PROSEG2BAYSOR": {
diff --git a/tests/default.nf.test b/tests/default.nf.test
index f1ef2bcf..1e6301e7 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     config "../conf/test.config"
 
-    test("-profile test") {
+    test("-profile test stub") {
 
         options "-stub"
 
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 134212cb..b913b700 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "-profile test": {
+    "-profile test stub": {
         "content": [
             {
                 "PROSEG2BAYSOR": {
diff --git a/tests/image_mode.nf.test b/tests/image_mode.nf.test
index dec9adaf..000faeb9 100644
--- a/tests/image_mode.nf.test
+++ b/tests/image_mode.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     config "../conf/test_image_mode.config"
 
-    test("-profile test") {
+    test("-profile test stub") {
 
         options "-stub"
 
diff --git a/tests/image_mode.nf.test.snap b/tests/image_mode.nf.test.snap
index 2512e272..50366f0a 100644
--- a/tests/image_mode.nf.test.snap
+++ b/tests/image_mode.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "-profile test": {
+    "-profile test stub": {
         "content": [
             {
                 "BAYSOR_PREPROCESS_TRANSCRIPTS": {
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 21d5c006..eff6fcbb 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -4,7 +4,6 @@
 ========================================================================================
 */
 
-// TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
diff --git a/tests/preview_mode.nf.test b/tests/preview_mode.nf.test
index 39fbb8c5..fe206319 100644
--- a/tests/preview_mode.nf.test
+++ b/tests/preview_mode.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     config "../conf/test_preview_mode.config"
 
-    test("-profile test") {
+    test("-profile test stub") {
 
         options "-stub"
 
diff --git a/tests/preview_mode.nf.test.snap b/tests/preview_mode.nf.test.snap
index 0f542673..e1c92907 100644
--- a/tests/preview_mode.nf.test.snap
+++ b/tests/preview_mode.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "-profile test": {
+    "-profile test stub": {
         "content": [
             {
                 "BAYSOR_CREATE_DATASET": {
@@ -45,17 +45,16 @@
                 "preview/untar/test_run/morphology.ome.tif",
                 "preview/untar/test_run/transcripts.parquet",
                 "preview/utility",
+                "preview/utility/parquet_to_csv",
+                "preview/utility/parquet_to_csv/test_run",
+                "preview/utility/parquet_to_csv/test_run/transcripts.parquet.csv",
                 "preview/utility/preview_data",
                 "preview/utility/preview_data/test_run",
                 "preview/utility/preview_data/test_run/gene_structure_mqc.tsv",
                 "preview/utility/preview_data/test_run/noise_distribution_mqc.tsv",
                 "preview/utility/preview_data/test_run/noise_level_mqc.png",
                 "preview/utility/preview_data/test_run/transcript_plots_mqc.png",
-                "preview/utility/preview_data/test_run/umap_mqc.tsv",
-                "preview/utility/spatialconverter",
-                "preview/utility/spatialconverter/parquet_to_csv",
-                "preview/utility/spatialconverter/parquet_to_csv/test_run",
-                "preview/utility/spatialconverter/parquet_to_csv/test_run/transcripts.parquet.csv"
+                "preview/utility/preview_data/test_run/umap_mqc.tsv"
             ],
             [
                 "sampled_transcripts.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -67,18 +66,18 @@
                 "gene_panel.json:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "morphology.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "transcripts.parquet:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "transcripts.parquet.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "gene_structure_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "noise_distribution_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "noise_level_mqc.png:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "transcript_plots_mqc.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "umap_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "transcripts.parquet.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "umap_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-04-29T19:23:42.749448196",
+        "timestamp": "2026-04-30T19:00:29.84624323",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/segfree_mode.nf.test b/tests/segfree_mode.nf.test
index ece296bd..2319b6e2 100644
--- a/tests/segfree_mode.nf.test
+++ b/tests/segfree_mode.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     config "../conf/test_segfree_mode.config"
 
-    test("-profile test") {
+    test("-profile test stub") {
 
         options "-stub"
 
diff --git a/tests/segfree_mode.nf.test.snap b/tests/segfree_mode.nf.test.snap
index bb13b3ea..98326c02 100644
--- a/tests/segfree_mode.nf.test.snap
+++ b/tests/segfree_mode.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "-profile test": {
+    "-profile test stub": {
         "content": [
             {
                 "BAYSOR_PREPROCESS_TRANSCRIPTS": {
diff --git a/workflows/spatialxe.nf b/workflows/spatialxe.nf
index 28dafede..71047930 100644
--- a/workflows/spatialxe.nf
+++ b/workflows/spatialxe.nf
@@ -43,7 +43,7 @@ include { XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE } from '../subworkflo
 // spatialdata subworkflows
 include { SPATIALDATA_WRITE_META_MERGE                     } from '../subworkflows/local/spatialdata_write_meta_merge/main'
 
-// TODO qc layer subworkflows
+// qc layer subworkflows
 include { OPT_FLIP_TRACK_STAT                              } from '../subworkflows/local/opt_flip_track_stat/main'
 
 /*
@@ -64,29 +64,29 @@ workflow SPATIALXE {
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    ch_versions = Channel.empty()
-
-    ch_input = Channel.empty()
-    ch_config = Channel.empty()
-    ch_features = Channel.value([])
-    ch_raw_bundle = Channel.empty()
-    ch_gene_panel = Channel.empty()
-    ch_qc_reports = Channel.empty()
-    ch_bundle_path = Channel.empty()
-    ch_preview_html = Channel.empty()
-    ch_exp_metadata = Channel.empty()
-    ch_gene_synonyms = Channel.empty()
-    ch_multiqc_files = Channel.empty()
-    ch_multiqc_report = Channel.empty()
-    ch_qupath_polygons = Channel.empty()
-    ch_morphology_image = Channel.empty()
-    ch_redefined_bundle = Channel.empty()
-    ch_coordinate_space = Channel.empty()
-    ch_panel_probes_fasta = Channel.empty()
-    ch_transcripts_file = Channel.empty()
-    ch_reference_annotations = Channel.empty()
-    ch_multiqc_pre_xr_report = Channel.empty()
-    ch_multiqc_post_xr_report = Channel.empty()
+    ch_versions = channel.empty()
+
+    ch_input = channel.empty()
+    ch_config = channel.empty()
+    ch_features = channel.value([])
+    ch_raw_bundle = channel.empty()
+    ch_gene_panel = channel.empty()
+    ch_qc_reports = channel.empty()
+    ch_bundle_path = channel.empty()
+    ch_preview_html = channel.empty()
+    ch_exp_metadata = channel.empty()
+    ch_gene_synonyms = channel.empty()
+    ch_multiqc_files = channel.empty()
+    ch_multiqc_report = channel.empty()
+    ch_qupath_polygons = channel.empty()
+    ch_morphology_image = channel.empty()
+    ch_redefined_bundle = channel.empty()
+    ch_coordinate_space = channel.empty()
+    ch_panel_probes_fasta = channel.empty()
+    ch_transcripts_file = channel.empty()
+    ch_reference_annotations = channel.empty()
+    ch_multiqc_pre_xr_report = channel.empty()
+    ch_multiqc_post_xr_report = channel.empty()
 
 
     /*
@@ -95,7 +95,6 @@ workflow SPATIALXE {
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    // TODO: Replace with params.test_data_mode for robustness
     if (workflow.profile.contains('test')) {
 
         // get sample, xenium bundle and image path
@@ -191,7 +190,7 @@ workflow SPATIALXE {
     }
 
     // get baysor xenium config
-    ch_config = Channel.fromPath(
+    ch_config = channel.fromPath(
             "${projectDir}/assets/config/xenium.toml",
             checkIfExists: true
         )
@@ -199,7 +198,7 @@ workflow SPATIALXE {
 
     // get segmentation mask if provided with --segmentation_mask for the baysor method
     if (params.segmentation_mask) {
-        ch_segmentation_mask = Channel.fromPath(
+        ch_segmentation_mask = channel.fromPath(
                 params.segmentation_mask,
                 checkIfExists: true
             )
@@ -208,12 +207,12 @@ workflow SPATIALXE {
 
     // get a list of features if provided with the --features for the ficture method
     ch_features = params.features
-        ? Channel.fromPath(params.features, checkIfExists: true).flatten()
-        : Channel.value([])
+        ? channel.fromPath(params.features, checkIfExists: true).flatten()
+        : channel.value([])
 
     // get custom cellpose model if provided with the --cellpose_model for the cellpose method
     if (params.cellpose_model) {
-        ch_cellpose_model = Channel.fromPath(
+        ch_cellpose_model = channel.fromPath(
                 params.cellpose_model,
                 checkIfExists: true
             )
@@ -222,7 +221,7 @@ workflow SPATIALXE {
 
     // get panel probes fasta for off-target-probe tracking
     if (params.probes_fasta) {
-        ch_panel_probes_fasta = Channel.fromPath(
+        ch_panel_probes_fasta = channel.fromPath(
                 params.probes_fasta,
                 checkIfExists: true
             )
@@ -231,7 +230,7 @@ workflow SPATIALXE {
 
     // get reference annotation files (gff,fa) for off-target-probe tracking
     if (params.reference_annotations) {
-        ch_reference_annotations = Channel.fromPath(
+        ch_reference_annotations = channel.fromPath(
                 "${params.reference_annotations}/*.{fa,gff}".toString(),
                 checkIfExists: true
             )
@@ -240,7 +239,7 @@ workflow SPATIALXE {
 
     // get gene synonyms for off-target-probe tracking
     if (params.gene_synonyms) {
-        ch_gene_synonyms = Channel.fromPath(
+        ch_gene_synonyms = channel.fromPath(
                 params.gene_synonyms,
                 checkIfExists: true
             )
@@ -249,7 +248,7 @@ workflow SPATIALXE {
 
     // get qupath ploygons
     if (params.qupath_polygons) {
-        ch_qupath_polygons = Channel.fromPath(
+        ch_qupath_polygons = channel.fromPath(
                 "${params.qupath_polygons}/*.geojson",
                 checkIfExists: true
             )
@@ -443,7 +442,7 @@ workflow SPATIALXE {
                       "For tiled Baysor, use baysor_prior='cells' (column-based)."
             }
 
-            ch_prior_mask = Channel.empty()
+            ch_prior_mask = channel.empty()
 
             BAYSOR_RUN_TRANSCRIPTS_PARQUET(
                 ch_bundle_path,
@@ -549,18 +548,18 @@ workflow SPATIALXE {
         SPATIALXE - MultiQC
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
-    ch_multiqc_config = Channel.fromPath(
+    ch_multiqc_config = channel.fromPath(
         "${projectDir}/assets/multiqc_config.yml",
         checkIfExists: true
     )
 
     ch_multiqc_custom_config = params.multiqc_config
-        ? Channel.fromPath(params.multiqc_config, checkIfExists: true)
-        : Channel.empty()
+        ? channel.fromPath(params.multiqc_config, checkIfExists: true)
+        : channel.empty()
 
     ch_multiqc_logo = params.multiqc_logo
-        ? Channel.fromPath(params.multiqc_logo, checkIfExists: true)
-        : Channel.empty()
+        ? channel.fromPath(params.multiqc_logo, checkIfExists: true)
+        : channel.empty()
 
     // Combine default and custom configs into a single list for the tuple-based MULTIQC input
     ch_multiqc_configs = ch_multiqc_config.mix(ch_multiqc_custom_config).collect()
@@ -570,7 +569,7 @@ workflow SPATIALXE {
         parameters_schema: "nextflow_schema.json"
     )
 
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
 
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')
@@ -580,7 +579,7 @@ workflow SPATIALXE {
         ? file(params.multiqc_methods_description, checkIfExists: true)
         : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
 
-    ch_methods_description = Channel.value(
+    ch_methods_description = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description)
     )
 
@@ -636,7 +635,6 @@ workflow SPATIALXE {
         // get the qc htmls if qc mode is run
         if (params.mode == 'qc' || params.run_qc) {
 
-            // TODO collect all qc outs in a channel to be passed to multiqc
             ch_multiqc_files = ch_multiqc_files.mix(
                 ch_qc_reports.map { _meta, qc_reports -> qc_reports }.collect().ifEmpty([])
             )