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Add README badge to pipeline documentation to pipeline template #4288

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1cdc9d5
Add README badge for docs
jfy133 May 19, 2026
501613c
Update CHANGELOG
jfy133 May 19, 2026
6a5c27d
Update nf_core/pipeline-template/README.md
jfy133 May 19, 2026
012211f
[automated] Fix code linting
nf-core-bot May 19, 2026
c1d179a
Simplify and re-structure badges: removes
jfy133 May 20, 2026
b0e3904
Try to escape jiner tags in etst string
jfy133 May 20, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@
### Template

- add `process_low_memory` resource label to `base.config` ([#4264](https://github.com/nf-core/tools/pull/4264))
- add README badge with link to full pipeline documentation on website ([#4288](https://github.com/nf-core/tools/pull/4288))

#### Version updates

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39 changes: 19 additions & 20 deletions nf_core/pipeline-template/README.md
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Expand Up @@ -12,29 +12,28 @@
# {{ name }}

{% endif -%}
{% if github_badges -%}
{% if codespaces %}[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/{{ name }}){% endif %}
[![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/nf-test.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/{{ name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/linting.yml){% endif -%}
{% if is_nfcore -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
{%- if github_badges -%}
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![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-{{ nf_core_version }}-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/{{ nf_core_version }})
[![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/)
[![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/{{ name }})

{% endif -%}
<!-- Meta data, citations etc. badges -->

{% if github_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/){% endif -%}
[![{% if github_badges -%}nf-core template version](https://img.shields.io/badge/nf--core_template-{{ nf_core_version }}-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/{{ nf_core_version }}){% endif -%}
{% if github_badges -%}[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX){% endif -%}

<!-- Documentation and launch badges -->

[![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/{{ short_name }}/usage)](https://nf-co.re/{{ short_name }}/usage)
{% if is_nfcore -%}[![AWS CI](https://img.shields.io/badge/see-example%20results-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
{%- if is_nfcore -%}[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23{{ short_name }}-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
{%- if is_nfcore -%}[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re){% endif -%}
{%- if is_nfcore -%}[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core){% endif -%}
{%- if is_nfcore -%}[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
{% if github_badges -%}![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/{{ name }}){% endif -%}
{% if github_badges -%}{% if codespaces %}[![Develop in GitHub Codespaces](https://img.shields.io/badge/develop-GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/{{ name }}){% endif %}{% endif -%}

{% endif -%}
<!-- Execution, Reproducibility, and CI status etc. badges -->

{% if github_badges -%}[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/){% endif -%}
{% if github_badges -%}[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/){% endif -%}
{% if github_badges -%}[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/){% endif -%}
{% if github_badges -%}[![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/nf-test.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/nf-test.yml){% endif -%}
{% if github_badges -%}[![GitHub Actions Linting Status](https://github.com/{{ name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/linting.yml){% endif -%}

## Introduction

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4 changes: 2 additions & 2 deletions tests/pipelines/test_bump_version.py
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Expand Up @@ -69,8 +69,8 @@ def test_bump_nextflow_version(self):
with open(new_pipeline_obj._fp("README.md")) as fh:
readme = fh.read().splitlines()
assert (
f"[![Nextflow](https://img.shields.io/badge/version-%E2%89%A5{version}-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)]"
"(https://www.nextflow.io/)" in readme
f"{{% if github_badges -%}}[![Nextflow](https://img.shields.io/badge/version-%E2%89%A5{version}-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/){{% endif -%}}"
in readme
)

def test_bump_pipeline_version_in_snapshot(self):
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