Adding Beagle v5.2

[gichas]

PR checklist

• 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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/phaseimpute branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[LouisLeNezet]

Thanks for this contribution.
Could you fix it in the same way as the other PR ?

[LouisLeNezet]

This is a fine addition to the pipeline.
Here is some comments to improve it.
Could you also update the CHANGELOG in this PR in the same way as the minimac4 PR ?

[LouisLeNezet]

Just a few update but otherwise good to go !

[LouisLeNezet]

I couldn't merge this PR with the dev branch.
I therefore reproduced it in PR #210