diff --git a/.nf-core.yml b/.nf-core.yml
index e7ec0252..1e213b56 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -21,4 +21,4 @@ template:
outdir: .
skip_features:
- igenomes
- version: 1.0.0
+ version: 1.1.0dev
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 8cff5748..47566390 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
report_comment: >
- This report has been generated by the nf-core/spatialaxe analysis pipeline. For information about how to interpret these results, please see the documentation.
+ This report has been generated by the nf-core/spatialaxe analysis pipeline. For information about how to interpret these results, please see the documentation.
report_section_order:
"nf-core-spatialaxe-methods-description":
order: -1000
diff --git a/nextflow.config b/nextflow.config
index 99b638cc..cf75ae06 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -385,7 +385,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.04.0'
- version = '1.0.0'
+ version = '1.1.0dev'
doi = ''
}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index eb24c81a..e09dc9f3 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -21,9 +21,9 @@
{
"@id": "./",
"@type": "Dataset",
- "creativeWorkStatus": "Stable",
- "datePublished": "2026-05-27T11:36:27+00:00",
- "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/spatialaxe)\n[](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml)[](https://nf-co.re/spatialaxe/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/spatialaxe)\n\n[](https://nfcore.slack.com/channels/spatialaxe)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/spatialaxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium (and soon Atera) 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\n\n> [!NOTE]\n> We are currently extending 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/spatialaxe/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 \n\n`CELLPOSE -> BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode \n```\n\n### Run coordinate-based segmentation mode \n\n`PROSEG -> PROSEG2BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode coordinate\n```\n\n### Run segfree mode \n\n`BAYSOR_SEGFREE`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode segfree\n```\n\n### Run preview mode \n\n`BAYSOR_PREVIEW`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode preview\n```\n\n### Run just the quality control \n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --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/spatialaxe/usage) and the [parameter documentation](https://nf-co.re/spatialaxe/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/spatialaxe/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/spatialaxe/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/spatialaxe 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 `#spatialaxe` channel](https://nfcore.slack.com/channels/spatialaxe) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\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",
+ "creativeWorkStatus": "InProgress",
+ "datePublished": "2026-06-17T15:15:09+00:00",
+ "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/spatialaxe)\n[](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml)[](https://nf-co.re/spatialaxe/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/spatialaxe)\n\n[](https://nfcore.slack.com/channels/spatialaxe)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/spatialaxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium (and soon Atera) 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\n\n> [!NOTE]\n> We are currently extending 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/spatialaxe/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 \n\n`CELLPOSE -> BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode \n```\n\n### Run coordinate-based segmentation mode \n\n`PROSEG -> PROSEG2BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode coordinate\n```\n\n### Run segfree mode \n\n`BAYSOR_SEGFREE`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode segfree\n```\n\n### Run preview mode \n\n`BAYSOR_PREVIEW`\n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --mode preview\n```\n\n### Run just the quality control \n\n```bash\nnextflow run nf-core/spatialaxe \\\n -profile \\\n --input samplesheet.csv \\\n --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/spatialaxe/usage) and the [parameter documentation](https://nf-co.re/spatialaxe/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/spatialaxe/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/spatialaxe/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/spatialaxe 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- Krešimir Beštak (kbestak)\n- Matthias Hörtenhuber (mashehu)\n- Maxime Garcia (maxulysse)\n- Kübra Narcı (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 `#spatialaxe` channel](https://nfcore.slack.com/channels/spatialaxe) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\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"
@@ -31,6 +31,9 @@
{
"@id": "assets/"
},
+ {
+ "@id": "bin/"
+ },
{
"@id": "conf/"
},
@@ -43,6 +46,9 @@
{
"@id": "modules/"
},
+ {
+ "@id": "modules/local/"
+ },
{
"@id": "modules/nf-core/"
},
@@ -99,7 +105,7 @@
},
"mentions": [
{
- "@id": "#93095c81-90d0-4005-8fe8-257133b523b7"
+ "@id": "#7c4a8872-f8d4-4f4b-a7f2-c2754d484851"
}
],
"name": "nf-core/spatialaxe"
@@ -126,13 +132,19 @@
"SoftwareSourceCode",
"ComputationalWorkflow"
],
+ "creator": [
+ {
+ "@id": "https://orcid.org/0009-0008-2420-6464"
+ }
+ ],
"dateCreated": "",
- "dateModified": "2026-05-27T13:36:27Z",
+ "dateModified": "2026-06-17T17:15:09Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": [
"nf-core",
"nextflow",
"10x-genomics",
+ "atera",
"image-processing",
"spatial",
"spatial-data-analysis",
@@ -143,6 +155,11 @@
"license": [
"MIT"
],
+ "maintainer": [
+ {
+ "@id": "https://orcid.org/0009-0008-2420-6464"
+ }
+ ],
"name": [
"nf-core/spatialaxe"
],
@@ -154,10 +171,10 @@
},
"url": [
"https://github.com/nf-core/spatialaxe",
- "https://nf-co.re/spatialaxe/1.0.0/"
+ "https://nf-co.re/spatialaxe/dev/"
],
"version": [
- "1.0.0"
+ "1.1.0dev"
]
},
{
@@ -173,11 +190,11 @@
"version": "!>=25.04.0"
},
{
- "@id": "#93095c81-90d0-4005-8fe8-257133b523b7",
+ "@id": "#7c4a8872-f8d4-4f4b-a7f2-c2754d484851",
"@type": "TestSuite",
"instance": [
{
- "@id": "#662205d5-7986-4a2b-99ae-86639b5bf728"
+ "@id": "#3ab54b2a-9518-45a0-8008-3839d03402c0"
}
],
"mainEntity": {
@@ -186,7 +203,7 @@
"name": "Test suite for nf-core/spatialaxe"
},
{
- "@id": "#662205d5-7986-4a2b-99ae-86639b5bf728",
+ "@id": "#3ab54b2a-9518-45a0-8008-3839d03402c0",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/spatialaxe",
"resource": "repos/nf-core/spatialaxe/actions/workflows/nf-test.yml",
@@ -208,6 +225,11 @@
"@type": "Dataset",
"description": "Additional files"
},
+ {
+ "@id": "bin/",
+ "@type": "Dataset",
+ "description": "Scripts that must be callable from a pipeline process"
+ },
{
"@id": "conf/",
"@type": "Dataset",
@@ -228,6 +250,11 @@
"@type": "Dataset",
"description": "Modules used by the pipeline"
},
+ {
+ "@id": "modules/local/",
+ "@type": "Dataset",
+ "description": "Pipeline-specific modules"
+ },
{
"@id": "modules/nf-core/",
"@type": "Dataset",
@@ -313,6 +340,12 @@
"@type": "Organization",
"name": "nf-core",
"url": "https://nf-co.re/"
+ },
+ {
+ "@id": "https://orcid.org/0009-0008-2420-6464",
+ "@type": "Person",
+ "email": "khersameesh24@gmail.com",
+ "name": "Sameesh Kher"
}
]
}
\ No newline at end of file
diff --git a/tests/coordinate_mode.nf.test.snap b/tests/coordinate_mode.nf.test.snap
index 4967372e..72a452ec 100644
--- a/tests/coordinate_mode.nf.test.snap
+++ b/tests/coordinate_mode.nf.test.snap
@@ -24,7 +24,7 @@
"untar": 1.34
},
"Workflow": {
- "nf-core/spatialaxe": "v1.0.0"
+ "nf-core/spatialaxe": "v1.1.0dev"
},
"XENIUMRANGER_IMPORT_SEGMENTATION": {
"xeniumranger": "4.0.1.1"
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index d5946632..3289c2a0 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -24,7 +24,7 @@
"untar": 1.34
},
"Workflow": {
- "nf-core/spatialaxe": "v1.0.0"
+ "nf-core/spatialaxe": "v1.1.0dev"
},
"XENIUMRANGER_IMPORT_SEGMENTATION": {
"xeniumranger": "4.0.1.1"
diff --git a/tests/image_mode.nf.test.snap b/tests/image_mode.nf.test.snap
index 4b2c5d3a..a9b73c2c 100644
--- a/tests/image_mode.nf.test.snap
+++ b/tests/image_mode.nf.test.snap
@@ -30,7 +30,7 @@
"untar": 1.34
},
"Workflow": {
- "nf-core/spatialaxe": "v1.0.0"
+ "nf-core/spatialaxe": "v1.1.0dev"
},
"XENIUMRANGER_IMPORT_SEGMENTATION": {
"xeniumranger": "4.0.1.1"
diff --git a/tests/preview_mode.nf.test.snap b/tests/preview_mode.nf.test.snap
index e44ff636..3d364f04 100644
--- a/tests/preview_mode.nf.test.snap
+++ b/tests/preview_mode.nf.test.snap
@@ -18,7 +18,7 @@
"untar": 1.34
},
"Workflow": {
- "nf-core/spatialaxe": "v1.0.0"
+ "nf-core/spatialaxe": "v1.1.0dev"
}
},
[
diff --git a/tests/segfree_mode.nf.test.snap b/tests/segfree_mode.nf.test.snap
index af848bc6..ac663a43 100644
--- a/tests/segfree_mode.nf.test.snap
+++ b/tests/segfree_mode.nf.test.snap
@@ -12,7 +12,7 @@
"untar": 1.34
},
"Workflow": {
- "nf-core/spatialaxe": "v1.0.0"
+ "nf-core/spatialaxe": "v1.1.0dev"
}
},
[
![\"nf-core/spatialaxe\"](\"docs/images/nf-core-spatialaxe_logo_dark.png\"){kind=logo}
\n