Add Parabricks DeepVariant module

[HudoGriz]

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/raredisease 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>).
• Ensure the test suite passes (nextflow run . -profile test_singleton,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).

Description

This PR adds the parabricks/deepvariant module for GPU-accelerated variant calling in the nf-core/raredisease pipeline.

At the Clinical Institute of Special Laboratory Diagnostics, University Medical Centre Ljubljana, we have been using this implementation internally, as it significantly accelerates variant calling without introducing major differences in benchmark results compared to the CPU-based DeepVariant implementation.

We are contributing this module so that:

• Other users can benefit from GPU acceleration in their rare disease analyses.
• Our version control and maintenance can be unified within the nf-core framework.

Tests performed

We successfully ran the following tests:

nextflow run . -profile test,singularity,gpu --variant_caller parabricks_deepvariant --outdir test_results

nextflow run . -profile test_singleton,singularity,gpu --variant_caller parabricks_deepvariant --outdir test_results_singleton

We are happy to receive feedback on how this contribution can be better integrated and aligned with nf-core standards, as well as any recommendations for improving its adoption and usability across the wider community.

[ramprasadn]

Thanks for this PR @HudoGriz! Could you add a changelog entry for this PR?