From 1cdc9d504cdbc6621300f441376d3b1ac7dc16c3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 19 May 2026 16:41:23 +0200 Subject: [PATCH 1/6] Add README badge for docs --- nf_core/pipeline-template/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 57908aa578..ba728b9c85 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -22,7 +22,8 @@ [![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 }}) +[![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 }}) [![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) + [![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/) From 501613cf6d9921fedb0962edb9c15f53b7717490 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 19 May 2026 16:44:48 +0200 Subject: [PATCH 2/6] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 56398753fc..fd4af0c924 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 From 6a5c27d630cbf7a69fa6c3b1724b3d3060a6764d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 19 May 2026 17:00:49 +0200 Subject: [PATCH 3/6] Update nf_core/pipeline-template/README.md Co-authored-by: Maxime U Garcia --- nf_core/pipeline-template/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index ba728b9c85..6039f61c0f 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -22,7 +22,8 @@ [![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 }}) [![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) +[![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 }}) +[![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) [![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/) From 012211f4db78cb0f4b0a1a1312add56c57b279ea Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 19 May 2026 15:05:51 +0000 Subject: [PATCH 4/6] [automated] Fix code linting --- nf_core/pipeline-template/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 6039f61c0f..db67e60c7e 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -22,7 +22,7 @@ [![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 }}) +[![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 }}) [![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) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) From c1d179a6ded7e9a8ecf11127b60a9401bbb7a1b8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 20 May 2026 13:36:03 +0200 Subject: [PATCH 5/6] Simplify and re-structure badges: removes --- nf_core/pipeline-template/README.md | 39 +++++++++++++---------------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index db67e60c7e..8e35bc3249 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -12,31 +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 }}) -[![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) -[![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 -%} +{% 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 -%} + + + +[![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 -%} + + +{% 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 From b0e39040ff745375f2a9a47b2e13a1524ad6f07e Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 20 May 2026 13:49:14 +0200 Subject: [PATCH 6/6] Try to escape jiner tags in etst string --- tests/pipelines/test_bump_version.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py index 3f34c18533..f04374e39b 100644 --- a/tests/pipelines/test_bump_version.py +++ b/tests/pipelines/test_bump_version.py @@ -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):