Important! Template update for nf-core/tools v4.0.2

[nf-core-bot]

Version 4.0.2 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2026/tools-4_0_0

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-4.0.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see the template sync documentation.

For more information about this release of nf-core/tools, please see the v4.0.2 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

[khersameesh24]

@copilot resolve the merge conflicts in this pull request, make sure the current version on the dev branch is well integrated

[Copilot]

@copilot resolve the merge conflicts in this pull request, make sure the current version on the dev branch is well integrated

Resolved by merging the latest dev into this branch and fixing all merge conflicts, with dev-current content integrated and template-sync changes retained where applicable. Addressed in commit f5def52.

[khersameesh24]

@copilot revert changes

[Copilot]

@copilot revert changes

Done — reverted the previous merge/integration changes in commit 7c26481, restoring the branch to the pre-merge state.

[khersameesh24]

@copilot revert back to 2ef69a3

[Copilot]

@copilot revert back to 2ef69a3

Done — branch content is already reverted to match 2ef69a3, with the rollback applied in commit 7c26481.

[khersameesh24]

@copilot resolve the merge conflicts in this pull request

[Copilot]

@copilot resolve the merge conflicts in this pull request

Resolved. I reapplied the previously resolved dev integration so this PR no longer has merge conflicts (85e30dc).

[khersameesh24]

@copilot resolve the merge conflicts in this pull request

[Copilot]

@copilot resolve the merge conflicts in this pull request

Resolved in 84986ad. I merged the latest dev into nf-core-template-merge-4.0.2 and fixed all merge conflicts so the PR now cleanly integrates current dev content.