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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

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adamrtalbot
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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

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@adamrtalbot adamrtalbot changed the base branch from master to dev October 5, 2022 13:34
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ewels
ewels approved these changes Oct 5, 2022
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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
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Thank you! :)

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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.

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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
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@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
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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
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@mirpedrol mirpedrol mirpedrol approved these changes

@ewels ewels Awaiting requested review from ewels

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