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Add plink_fit_regenie subworkflow#11937

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lyh970817 wants to merge 8 commits into
nf-core:masterfrom
lyh970817:subworkflows/regenie-fit-create
Draft

Add plink_fit_regenie subworkflow#11937
lyh970817 wants to merge 8 commits into
nf-core:masterfrom
lyh970817:subworkflows/regenie-fit-create

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Description

Adds the plink_fit_regenie subworkflow to fit REGENIE Step 1 prediction models from PLINK-format genotype bundles.

This subworkflow supports the standard REGENIE Step 1 path and the chunked L0/L1 path, reusing existing REGENIE modules and shared human popgen test data.

Draft dependency: this PR depends on #11768 for regenie/runl1.

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!
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For subworkflows:
      • nf-core subworkflows test plink_fit_regenie --profile docker
      • nf-core subworkflows test plink_fit_regenie --profile singularity
      • nf-core subworkflows test plink_fit_regenie --profile conda

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