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Add BEAGLE5 imputation subworkflow #9550

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Merged
LouisLeNezet merged 20 commits into from
Dec 11, 2025
Merged

Add BEAGLE5 imputation subworkflow #9550

LouisLeNezet merged 20 commits into from
Dec 11, 2025

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@LouisLeNezet LouisLeNezet commented Dec 10, 2025

PR checklist

This PR add the last imputation subworkflow of phaseimpute.
It uses beagle5 imputation software.
The module beagle5 just needed to have the region as optional value to parallelize chromosome chunks.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@LouisLeNezet LouisLeNezet marked this pull request as ready for review December 10, 2025 20:31
@LouisLeNezet LouisLeNezet self-assigned this Dec 10, 2025
nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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@LouisLeNezet @nvnieuwk
Update subworkflows/nf-core/vcf_impute_beagle5/main.nf
a15d833 
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk reviewed Dec 11, 2025
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Some general comments, but looking good overall. Could you in the future split up this PR into 2 PRs. This will make the review process faster for both you and the reviewer :)

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LouisLeNezet commented Dec 11, 2025

Some general comments, but looking good overall. Could you in the future split up this PR into 2 PRs. This will make the review process faster for both you and the reviewer :)

I'm really sorry this was indeed mean for another PR, but I might have made a mistake when using git and I've merged two branch together.
I will remove the glimpse2 subworkflow.

nvnieuwk
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nvnieuwk commented Dec 11, 2025

I will remove the glimpse2 subworkflow.

That's not necessary for now, I already reviewed it. Just something to keep in mind for the future 🚀

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LouisLeNezet commented Dec 11, 2025

I will remove the glimpse2 subworkflow.

That's not necessary for now, I already reviewed it. Just something to keep in mind for the future 🚀

Sorry, I saw your comment too late.
The PR was already in review in #9434

@LouisLeNezet LouisLeNezet added this pull request to the merge queue Dec 11, 2025
Merged via the queue into nf-core:master with commit 043c568 Dec 11, 2025
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@LouisLeNezet LouisLeNezet deleted the sbwf_beagle5 branch December 11, 2025 13:11
vagkaratzas pushed a commit that referenced this pull request Dec 12, 2025
@LouisLeNezet @nvnieuwk @vagkaratzas
Add BEAGLE5 imputation subworkflow (#9550)
e23f119 
* Update glimpse2 sbwf

* Update test

* Add region to beagle5

* Add subworkflow

* Fix linting

* Fix linting

* Fix linting

* Update subworkflows/nf-core/vcf_impute_beagle5/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Add comment

* Update grouping and test

* Remove tag

* Revert change glimpse2 reference

* Revert change glimpse2 sbwf

* Revert change glimpse2 sbwf

* Revert change glimpse2 sbwf

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@LouisLeNezet LouisLeNezet mentioned this pull request Dec 13, 2025
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