From 341ddd26c2f6e1de41f94e5cabc3ad0d28afcc15 Mon Sep 17 00:00:00 2001 From: f641l Date: Thu, 6 Aug 2026 16:04:47 +0200 Subject: [PATCH] bump dev version to 1.0.1dev --- .nf-core.yml | 2 +- CHANGELOG.md | 12 ++++++++++++ assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 28 ++++++++++------------------ 5 files changed, 25 insertions(+), 21 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 43484e56..352e6ed3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -22,4 +22,4 @@ template: outdir: . skip_features: - igenomes - version: 1.0.1 + version: 1.0.1dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 67f9bd0d..c3dbe4cf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 1.0.1dev - [date] + +Initial release of nf-core/spatialaxe, created with the [nf-core](https://nf-co.re/) template. + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## 1.0.1 - [06.08.2026] Hotfix to tackle some bugs diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 2e796b9a..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 eef01269..3f91e590 100644 --- a/nextflow.config +++ b/nextflow.config @@ -385,7 +385,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.04.0' - version = '1.0.1' + version = '1.0.1dev' doi = '' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 2ac72fc8..42e4dcd5 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-07-23T13:01:17+00:00", - "description": "

\n \n \n \"nf-core/spatialaxe\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialaxe)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialaxe/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/spatialaxe/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/spatialaxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialaxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialaxe)[![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/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![nf-core/spatialaxe-metromap](docs/images/spatialaxe-metromap.png)\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", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-08-06T14:03:08+00:00", + "description": "

\n \n \n \"nf-core/spatialaxe\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialaxe)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialaxe/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/spatialaxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.20733817-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.20733817)\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/spatialaxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialaxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialaxe)[![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/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![nf-core/spatialaxe-metromap](docs/images/spatialaxe-metromap.png)\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\nIf you use nf-core/spatialaxe for your analysis, please cite it using the following doi: [10.5281/zenodo.20733817](https://doi.org/10.5281/zenodo.20733817)\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" @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#261e6187-b79f-4b98-ba5b-c00684be47bc" + "@id": "#ae53c394-e66c-4071-90b6-f65fa2ca9cde" } ], "name": "nf-core/spatialaxe" @@ -136,9 +136,6 @@ { "@id": "https://orcid.org/0009-0008-2420-6464" }, - { - "@id": "#5fd4466e-7ce2-4d27-924e-ee46d6d24240" - }, { "@id": "https://orcid.org/0000-0002-3651-5685" } @@ -149,7 +146,7 @@ } ], "dateCreated": "", - "dateModified": "2026-07-23T15:01:17Z", + "dateModified": "2026-08-06T16:03:08Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -185,10 +182,10 @@ }, "url": [ "https://github.com/nf-core/spatialaxe", - "https://nf-co.re/spatialaxe/1.0.1/" + "https://nf-co.re/spatialaxe/dev/" ], "version": [ - "1.0.1" + "1.0.1dev" ] }, { @@ -204,11 +201,11 @@ "version": "!>=25.04.0" }, { - "@id": "#261e6187-b79f-4b98-ba5b-c00684be47bc", + "@id": "#ae53c394-e66c-4071-90b6-f65fa2ca9cde", "@type": "TestSuite", "instance": [ { - "@id": "#e58b049c-0f60-4176-ae4e-f6fd057d8c60" + "@id": "#c5acff29-7d94-4ad2-bdb8-b21c374cca24" } ], "mainEntity": { @@ -217,7 +214,7 @@ "name": "Test suite for nf-core/spatialaxe" }, { - "@id": "#e58b049c-0f60-4176-ae4e-f6fd057d8c60", + "@id": "#c5acff29-7d94-4ad2-bdb8-b21c374cca24", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/spatialaxe", "resource": "repos/nf-core/spatialaxe/actions/workflows/nf-test.yml", @@ -363,11 +360,6 @@ "name": "Sameesh Kher", "url": "https://github.com/khersameesh24" }, - { - "@id": "#5fd4466e-7ce2-4d27-924e-ee46d6d24240", - "@type": "Person", - "name": "Dongze He" - }, { "@id": "https://orcid.org/0000-0002-3651-5685", "@type": "Person",