Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

NF-Core Sync includes template.yaml as option #1880

Merged
merged 7 commits into from
Oct 12, 2022
Merged

NF-Core Sync includes template.yaml as option #1880

merged 7 commits into from
Oct 12, 2022

Conversation

adamrtalbot
Copy link
Contributor

Fixes #1879

Adds -t/--template-yaml to nf-core sync, so that users can update their pipeline based on existing template file.

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

@github-actions

This comment was marked as resolved.

Sign in to view
@adamrtalbot adamrtalbot changed the base branch from master to dev October 5, 2022 13:34
@adamrtalbot adamrtalbot force-pushed the 1879_sync_template_yaml branch from c0049b0 to ad6e31b Compare October 5, 2022 13:37
@codecov

This comment was marked as resolved.

Sign in to view
ewels
ewels approved these changes Oct 5, 2022
View reviewed changes
Copy link
Member

@ewels ewels left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice! This is all that was required? Great!

I'd like to wait for the CI tests to run / pass, but reading the code LGTM 👍🏻 (haven't tested running)

mirpedrol
mirpedrol approved these changes Oct 5, 2022
View reviewed changes
Copy link
Member

@mirpedrol mirpedrol left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thank you! :)

@adamrtalbot
Copy link
Contributor Author

I haven't added a new test - is that OK?

I'm sure there are lots of edge cases but it works with a quick demo pipeline.

@adamrtalbot
Copy link
Contributor Author

Actually - it gets in a mess if the template file is in the repository. Relatively easy fix.

Adam Talbot added 2 commits October 5, 2022 16:06
nf-core sync supports template.yaml within repository
713987a 
- Cache template.yml file before running nf-core sync.
- If syncing fails, reset to start
Merge branch '1879_sync_template_yaml' of github.com:adamrtalbot/tool…
341e573 
…s into 1879_sync_template_yaml
@adamrtalbot adamrtalbot requested review from ewels and mirpedrol October 5, 2022 16:09
@adamrtalbot
Copy link
Contributor Author

@ewels @mirpedrol Please re-review, I've updated the code to cache the template YAML and re-write it during syncing which is a bit more involved and has to catch some exceptions.

mirpedrol
mirpedrol approved these changes Oct 12, 2022
View reviewed changes
Copy link
Member

@mirpedrol mirpedrol left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for the updates, it looks good! Feel free to merge when tests pass :)

@mirpedrol mirpedrol merged commit 33726de into nf-core:dev Oct 12, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mirpedrol mirpedrol mirpedrol approved these changes

@ewels ewels Awaiting requested review from ewels

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

nf-core sync should support the template.yaml
3 participants
@adamrtalbot @ewels @mirpedrol