Request org details to fill in more template fields by muffato · Pull Request #4146 · nf-core/tools

muffato · 2026-03-29T20:25:26Z

My motivation is to make the RO-Crates more accurate by using actual correct org details (URL and full name). RO-Crates are automatically updated by the nf-core tooling at every template update, version bump. Fixing them every time is quite time consuming.
I introduce two new template parameters:

org_name: full name of the organisation (as opposite to org which is the name on GitHub)
org_url: organisation website

While doing it I realised that several template fields could benefit from the extra information and avoid wrongly pointing at https://nf-co.re. Looking into it, I then realised that you had just added {% if is_nfcore -%} blocks as a workaround for those wrong links :) so here I undo some of these thanks to the new org URL field.

Not all https://nf-co.re/ ocurrences need to be tuned to the org. Not all org websites will have pages like you have on https://nf-co.re/ . But all repos created by the tooling have doc/usage.md and docs/output.md, which can be accessed from the git web UI.
So here I take the approach of:

Using https://github.com/$org as the default URL
Changing all https://nf-co.re/{{ short_name }}/usage occurrences with the GitHub equivalent (+ support for other common forges), or else assuming the org URL supports { short_name }}/usage path (which we do ;) )

I collect the org URL and name in the pipelines create TUI, but only for non-nf-core pipelines (no need to burden official nf-core pipelines with the extra box.

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

codecov · 2026-03-29T20:26:48Z

Codecov Report

❌ Patch coverage is 95.53571% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.25%. Comparing base (3858865) to head (05c9fa9).

Files with missing lines	Patch %	Lines
nf_core/pipelines/rocrate.py	93.75%	3 Missing ⚠️
nf_core/pipelines/create/basicdetails.py	98.03%	1 Missing ⚠️
nf_core/pipelines/create/utils.py	88.88%	1 Missing ⚠️

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Copilot

Pull request overview

This PR adds organisation metadata (org_name, org_url) to the pipeline template config and uses it to generate more accurate RO-Crate publisher metadata and template documentation links (including forge-aware GitHub/GitLab/Bitbucket/Codeberg doc URLs).

Changes:

Add org_name / org_url fields, backfill logic for legacy .nf-core.yml, and helper utilities to compute org + docs URLs.
Update pipeline template files to use usage_url / output_url instead of hard-coded nf-co.re links in multiple places.
Extend and adjust test coverage for URL generation, RO-Crate metadata, template sync backfilling, and the create TUI behavior.

Reviewed changes

Copilot reviewed 19 out of 21 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
`nf_core/utils.py`	Adds org/docs URL helpers, new template config fields, and backfill for legacy configs.
`nf_core/pipelines/create/utils.py`	Validates `org_url` and requires org metadata fields in create config inputs.
`nf_core/pipelines/create/basicdetails.py`	Adds TUI inputs for org metadata and keeps them in sync with org until overridden.
`nf_core/pipelines/create/create.py`	Populates derived org metadata and injects `usage_url` / `output_url` into Jinja params.
`nf_core/pipelines/rocrate.py`	Uses template org metadata for RO-Crate publisher and attempts to source topics from org site.
`nf_core/pipelines/lint/multiqc_config.py`	Uses `org_url` + forge-aware output docs URLs for expected MultiQC report comment.
`nf_core/pipeline-template/README.md`	Switches usage/output links to `usage_url` / `output_url` variables.
`nf_core/pipeline-template/nextflow_schema.json`	Updates help text to reference `usage_url`.
`nf_core/pipeline-template/main.nf`	Prints website URL using `org_url` for all pipelines.
`nf_core/pipeline-template/docs/usage.md`	Replaces nf-core-only warning with org-aware link to `usage_url`.
`nf_core/pipeline-template/docs/README.md`	Replaces nf-core-conditional website text with org-aware `org_url`.
`nf_core/pipeline-template/docs/CONTRIBUTING.md`	Updates help links to use `usage_url` with nf-core Slack info conditional.
`nf_core/pipeline-template/assets/multiqc_config.yml`	Updates report comment to always link to `output_url`.
`nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml`	Uses `usage_url` for pipeline docs link (nf-core troubleshooting link stays conditional).
`tests/test_utils.py`	Adds parametrized tests for forge-aware docs URL helpers.
`tests/pipelines/test_sync.py`	Adds regression test ensuring legacy configs backfill `org_url` during template rebuild.
`tests/pipelines/test_rocrate.py`	Stabilizes git author history + adds RO-Crate tests for org metadata usage (with request mocking).
`tests/pipelines/test_create.py`	Extends create tests to assert org metadata defaults and propagated template links.
`tests/pipelines/test_create_app.py`	Adds TUI test for org metadata auto-fill/restore behavior + button helper.
`tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg`	Updates snapshot output after UI changes.
`tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg`	Updates snapshot output after UI changes.

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mashehu

We are in the middle of wrapping up a release and this feels like a bigger change to the template, so I will have a more thorough review after this release

muffato · 2026-03-31T09:30:55Z

No pb. I still need to go through the comments made by Copilot in this PR and the other one.

This allows testing the creator entity

…g org name

muffato self-assigned this Mar 29, 2026

muffato force-pushed the org_details branch 5 times, most recently from 0b9cffe to 88d714f Compare March 31, 2026 02:12

muffato marked this pull request as ready for review March 31, 2026 07:35

Copilot AI review requested due to automatic review settings March 31, 2026 07:35

Copilot started reviewing on behalf of muffato March 31, 2026 07:36 View session

Copilot AI reviewed Mar 31, 2026

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Comment thread nf_core/pipelines/lint/multiqc_config.py Outdated

Comment thread nf_core/pipelines/rocrate.py Outdated

Comment thread nf_core/pipelines/rocrate.py Outdated

Comment thread nf_core/pipelines/rocrate.py Outdated

mashehu reviewed Mar 31, 2026

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Comment thread nf_core/utils.py Outdated

mashehu reviewed Mar 31, 2026

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Comment thread nf_core/utils.py

mashehu reviewed Mar 31, 2026

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mashehu added this to the 4.1.0 milestone Mar 31, 2026

muffato mentioned this pull request Mar 31, 2026

Minor template fixes #4145

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4 tasks

muffato force-pushed the org_details branch from 56829e9 to 907343e Compare March 31, 2026 23:52

muffato deleted the branch dev April 3, 2026 01:10

muffato closed this Apr 3, 2026

muffato reopened this Apr 5, 2026

muffato changed the base branch from template to dev April 5, 2026 00:39

muffato force-pushed the org_details branch 2 times, most recently from 19cbd55 to ace83da Compare April 5, 2026 00:43

muffato marked this pull request as draft April 5, 2026 09:17

muffato force-pushed the org_details branch 5 times, most recently from b6eba81 to 6589cdd Compare April 7, 2026 02:02

muffato added 10 commits April 20, 2026 23:58

Store the org URL in the nf-core config file

ee55460

Also collect the org name

2cc2e84

Only sync the name and URL fields when editing the gihub org name

b82c220

Functioning usage URLs for GitHub sites

c8a9c7b

Expanded to cover output docs

7ff42b4

Revive the default values when loading config files

d2ee60b

Snapshot update

5d095ad

Get the org name from the config file

a8b2a8f

Store the org URL in the nf-core config file

069497c

Also collect the org name

4b0610c

muffato force-pushed the org_details branch from e0c3930 to 260afb1 Compare April 20, 2026 23:13

muffato added 12 commits April 21, 2026 00:41

Embed org_url in the rocrate and mock internet requests

8ef8b72

Don't use real author names in tests

74ca2f7

This allows testing the creator entity

More optimal rocrate config loading

5a1eb77

Don't fail if the org doesn't provide a JSON

579d71c

Renamed org_name to org_full_name to avoid confusion with the existin…

e27245f

…g org name

Combined the function to generate docs URLs

993f00a

Factored out some code to access template parameters

3c4d062

New function to get link to the pipeline page

6e401ef

Better URLs for tagged releases

435a36b

Fixedand expanded the tests

5a98c8d

bug: the URL was meant to be added the list

9d41f78

[lint] os.listdir is to be avoided

05c9fa9

muffato force-pushed the org_details branch from 260afb1 to 05c9fa9 Compare April 20, 2026 23:45

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Request org details to fill in more template fields#4146

Request org details to fill in more template fields#4146
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muffato commented Mar 29, 2026 •

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