Automatic template sync appears to have stopped for nf-core/gwas after nf-core/tools v3.2.1

[lyh970817]

Description of the bug

Summary

Automatic nf-core template sync appears to have stopped for nf-core/gwas after the nf- core/tools v3.2.1 sync on 2025-04-30.

Since then, template updates seem to have been handled manually on dev, while the
upstream TEMPLATE branch has not advanced.

Evidence

• The current upstream TEMPLATE tip is still:

  • commit f3514e2
  • message: Template update for nf-core/tools version 3.2.1
  • date: 2025-04-30

• The last bot-opened template PR appears to be:

  • #65
  • Important! Template update for nf-core/tools v3.2.1
  • opened 2025-04-30
  • closed unmerged 2025-05-13

• On 2025-05-13, #65 was closed with the
  comment:

  • “Closing as we're just starting with a fresh template”

• Around the same time, a manual commit was added:

  • commit 186e716
  • initial template build from nf-core/tools, version 3.2.1

• In March 2026, template updates were handled manually:

  • #73
  • #74

What I checked

• TEMPLATE exists upstream.
• dev still shares git history with TEMPLATE.
• Protected TEMPLATE branches are normal in other nf-core repos and do not by themselves
  prevent automatic sync PRs.
• The old master / dev divergence is probably not the cause, because bot-opened
  template PRs continued for a long time after [First dev release with qc subworkflow #17](https://github.com/nf-core/gwas/
  pull/17).

Likely issue

The remaining likely explanation is that nf-core/gwas stopped being updated by the
external nf-core sync automation at the step where TEMPLATE is regenerated and pushed.

Possible causes:

• the repo is being skipped by the sync automation
• the automation app/bot no longer has the required permission or bypass on TEMPLATE
• the May 2025 manual “fresh template” intervention changed repo state in a way the
  automation no longer handles correctly

Request

Could someone with access to the nf-core sync automation check why nf-core/gwas:TEMPLATE
stopped updating after commit f3514e2 on 2025-04-30?

In particular:

• Was nf-core/gwas skipped by the sync automation after later nf-core/tools releases?
• Did the automation fail to push to TEMPLATE for this repo?
• Is there any repo-specific setting or protection rule preventing the sync bot/app from
  updating TEMPLATE?

Command used and terminal output

Relevant files

No response

System information

No response