Adding Minimac4 to phaseimpute

[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: 3.3.1.
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.

[gichas]

Summary of Changes

Added MINIMAC4 support to nf-core/phaseimpute pipeline:

New modules:

• minimac4/compressref - Compresses reference panels to MSAV format
• minimac4/impute - Performs genotype imputation

New subworkflow:

• vcf_impute_minimac4 - Complete MINIMAC4 imputation workflow

Integration:

• Added MINIMAC4 to main workflow with proper chromosome handling
• Updated schema validation to include minimac4 as valid tool
• Added test profile test_minimac4

Testing:

• nf-test coverage for modules and subworkflows
• Integration tests with test datasets

Ready for review

[LouisLeNezet]

Just a few changes needed, but good work otherwise !
You also need to update the CHANGELOG.md, add the dependencies and yourself in the contributors.

[LouisLeNezet]

Can you fix the merging conflict ?

[LouisLeNezet]

There seems to be an issue with how the file was modified.
Did you perhaps modified the file on windows ?
This might cause a change in the newline character.

[LouisLeNezet]

Just a few changes before approving !

Could you add the description in the usage.md ?

[LouisLeNezet]

Just a little addition needed for the documentation

[LouisLeNezet]

Please update the - --tools [glimpse1, glimpse2, quilt, stitch]: A selection of one or more of the available imputation tools.

[LouisLeNezet]

LGTM

[LouisLeNezet]

Similarly to beagle5.
All this work have been transferred to a new PR #211 to fix the merging issues.