Add README badge to pipeline documentation to pipeline template

[jfy133]

Based on a valid reviewer comment on a nf-core/mag manuscript:

3. It would be useful to have a link to the documentation prominently displayed at the top of the README. It's in the "About" section of the repo, but it would be nice to have amongst all the badges

Reviewing the README file, it does take a long time to get to the first link to the full documentation (in nf-core/mag, it's in the 'Usage' section, and you've already scrolled through piepline description, metromap etc... for example).

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[mashehu]

I don't think this will be that visible in the forest of badges... but if you think it helps

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.30%. Comparing base (4c78254) to head (b0e3904).

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[jfy133]

I don't think this will be that visible in the forest of badges... but if you think it helps

It might be difficult, but I think this would be more useful than many of the badges we have... If we wanted to do a cull re/order, I think we could do a restructure:

• Nextflow version + nf-core template version + documentation + (renamed) full test) + Slack
• Run with `{conda,docker,singularity}
• Open in Codespaces + Launch Seqera Platform
• Zenodo + Citation

I would drop unit tests, and all the social media ones, as these are not pipeline specific...

What do you think?

[jfy133]

@nf-core-bot fix linting

[github-actions]

⚠️ Cannot proceed with deployment

• reviewDecision: APPROVED
• commitStatus: FAILURE

Your pull request is approved but CI checks are failing

[jfy133]

OK I'll try on mag as a demo and report back here

[jfy133]

Changes after discussions with maintainers ¹:

• I've tried to remove stuff I didn't feel was relevant (duplicate unit test, social media), and collapse into relevant categories (see labels)
• Iv'e added a badge to access to the documentation
• Renamed some (e.g. the AWS megatest outputs, singularity to apptainer etc.)

Final version should look somethign like this (note MAG has 3 extra badges for publication, HiRSE and BIgMAG):

Note that I've tried to clean up the jinjer if/else statement blocks too, the current one was extremely messy... I hope I've done it right... I tried to base it on me taking the dev version of teh badges section, and tried to work out which end-if is derived from which tag using indentation:

{% 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 -%}

{%- 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){% endif -%}

Footnotes

1. https://nfcore.slack.com/archives/C043UU89KKQ/p1779270013207999 ↩

[jfy133]

I guess the test_bump_version test is failing as I've added strings at the beginning/end of the line, but I'm not sure how to escape the jinjer tags in the test assert...