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Merged
jfy133 merged 9 commits into from
May 20, 2026
+18 −12
Merged

Simplify badges further #1038

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57abfd6
Simplify badges
jfy133 May 20, 2026
83573b3
Add missing zenodo badge
jfy133 May 20, 2026
08b1606
Add missing CI badge
jfy133 May 20, 2026
c219d50
Add content
jfy133 May 20, 2026
b03ccf8
Reshuffle
jfy133 May 20, 2026
29c9b98
Make formatting consistent
jfy133 May 20, 2026
778434d
First HIRSE logo
jfy133 May 20, 2026
e3dbf34
Switch singulariy to apptainer
jfy133 May 20, 2026
1870ba5
After feedback from @maxulysse and @mashehu
jfy133 May 20, 2026
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30 changes: 18 additions & 12 deletions README.md
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</picture>
</h1>

[![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/mag)
[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3589527)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007)
<!-- Meta data and citations badges -->

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2) [![nf-core/documentation](https://img.shields.io/badge/See-full_documentation-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re/mag/usage)](https://nf-co.re/mag/usage)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
[![Cite Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3589527)
[![Cite Publication](https://img.shields.io/badge/cite%20-Publication-orange)](https://doi.org/10.1093/nargab/lqac007)
![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?label=HiRSE&labelColor=005aa0&link=go.fzj.de/CodePromo) [![Static Badge](https://img.shields.io/badge/%F0%9F%8D%94%20%20BIgMAG-compatible-%2324B064)](https://github.com/jeffe107/BIgMAG)

<!-- Documentation and launch -->

[![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/mag)
[![nf-core/documentation](https://img.shields.io/badge/read-documentation-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re/mag/usage)](https://nf-co.re/mag/usage)
[![AWS CI](https://img.shields.io/badge/see-example%20results-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)
[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)
[![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/mag)
[![Develop GitHub Codespaces](https://img.shields.io/badge/develop-GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core-mag)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)[![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)
<!-- Execution, Reproducibility, and CI status -->

![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo) [![Static Badge](https://img.shields.io/badge/%F0%9F%8D%94%20%20BIgMAG-compatible-%2324B064)](https://github.com/jeffe107/BIgMAG)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with apptainer](https://img.shields.io/badge/run%20with-apptainer-fc9114.svg?labelColor=000000)](https://apptainer.org/documentation/)
[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/linting.yml)

## Introduction

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