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Add REGENIE chunked step 1 modules#11739

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lyh970817 wants to merge 17 commits into
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lyh970817:modules/regenie-step1-chunks-create
Draft

Add REGENIE chunked step 1 modules#11739
lyh970817 wants to merge 17 commits into
nf-core:masterfrom
lyh970817:modules/regenie-step1-chunks-create

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REGENIE is a C++ program for whole-genome regression modelling of large GWAS cohorts. This PR adds a chunked Step 1 module family that exposes REGENIE's native level-0 parallelization workflow:

  • regenie/splitl0 creates the level-0 split master file and per-job SNP lists.
  • regenie/runl0 runs one level-0 job from the split master file.
  • regenie/runl1 gathers the level-0 outputs and finishes Step 1, producing the standard prediction list and LOCO files consumed by regenie/step2.

This PR depends on the base regenie/step1 module in #11008.

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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • 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.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test regenie/splitl0 --profile docker
      • nf-core modules test regenie/runl0 --profile docker
      • nf-core modules test regenie/runl1 --profile docker
      • nf-core modules test regenie/splitl0 --profile singularity
      • nf-core modules test regenie/runl0 --profile singularity
      • nf-core modules test regenie/runl1 --profile singularity
      • nf-core modules test regenie/splitl0 --profile conda
      • nf-core modules test regenie/runl0 --profile conda
      • nf-core modules test regenie/runl1 --profile conda

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