[DRAFT] Feature/ploidy support

[zhliUU]

[DRAFT]: Add per-sample ploidy support for HaplotypeCaller

Summary

• Add ploidy column to input schema (integer, default: 2, minimum: 1)
• Pass ploidy to HaplotypeCaller via --sample-ploidy in ext.args
• Add test profiles and CSV files for haploid (ploidy=1) and triploid (ploidy=3)
• Skip VCFtools for polyploid samples (ploidy > 2) since VCFtools TsTv does not support polyploid genotypes

Discussion: Per-sample vs global ploidy

This PR introduces per-sample ploidy via the input CSV. This differs from existing global parameters like ascat_ploidy and cf_ploidy.

Per-sample ploidy (CSV input):

• Allows mixed ploidy samples in one run
• More accurate for heterogeneous datasets
• Currently implemented for: HaplotypeCaller

Global ploidy (parameters):

• Simpler for uniform datasets
• Currently used by power users: ASCAT (ascat_ploidy to override optimization), ControlFREEC (cf_ploidy "type": "string")

Questions for maintainers:

1. Should we keep both approaches (per-sample CSV + global parameter)?
2. Should per-sample ploidy be extended to other tools (FreeBayes, CNVkit, TIDDIT)?
3. How should per-sample ploidy interact with existing global parameters?

Changes

File	Description
assets/schema_input.json	Add ploidy field (integer, default: 2, min: 1)
conf/modules/haplotypecaller.config	Pass --sample-ploidy to GATK4_HAPLOTYPECALLER
conf/modules/modules.config	Skip VCFTOOLS for ploidy > 2
conf/test/tools_germline_haploid.config	Test profile for haploid samples
conf/test/tools_germline_triploid.config	Test profile for triploid samples
nextflow.config	Register new test profiles
tests/csv/3.0/recalibrated_germline_*.csv	Test input CSVs with ploidy column

Test plan

• Test haploid sample (ploidy=1):

  nextflow run . -profile test,tools_germline_haploid,docker \
    --outdir results_haploid \
    --tools haplotypecaller \
    --skip_tools haplotypecaller_filter \
    -resume

• Test triploid sample (ploidy=3):

  nextflow run . -profile test,tools_germline_triploid,docker \
    --outdir results_triploid \
    --tools haplotypecaller \
    --skip_tools haplotypecaller_filter \
    -resume

• Verify VCFtools is skipped for triploid samples

• Verify default ploidy=2 works for existing pipelines (backwards compatible: nextflow run . -profile test,docker --outdir <OUTDIR>).

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/sarek 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).