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Add ldak/reml module#12302

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lyh970817 wants to merge 1 commit into
nf-core:masterfrom
lyh970817:ldak-reml
Draft

Add ldak/reml module#12302
lyh970817 wants to merge 1 commit into
nf-core:masterfrom
lyh970817:ldak-reml

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This PR adds the ldak/reml module — Run linkage disequilibrium-adjusted kinship (LDAK) restricted maximum likelihood (REML) heritability estimation on a precomputed genomic relationship matrix (GRM) and phenotype. It upstreams main.nf, meta.yml, environment.yml, and nf-test tests (including a stub), with topic-based version reporting, and snapshots the full output contract via sanitizeOutput. Tests reuse the existing public plink_simulated fixtures from nf-core/test-datasets; no new test data required.

Draft — stacked submission. This module's nf-test setup{} builds fixtures by running upstream LDAK modules, so this branch also includes its prerequisite module(s) — ldak/addgrms, ldak/calckins, ldak/createthinweights, ldak/filterrelatedness, ldak/thinpredictors — in the diff against master (stacked-by-inclusion). Those will drop out as their own PRs merge. Kept as a draft until the prerequisites land; only Docker has been run so far (Singularity/Conda to follow).

  • 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 (not necessary — reuses existing plink_simulated fixtures).
  • 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 ldak/reml --profile docker
      • nf-core modules test ldak/reml --profile singularity
      • nf-core modules test ldak/reml --profile conda

Primary module: ldak/reml. Bundled test-dependency modules: addgrms calckins createthinweights filterrelatedness thinpredictors.
Ported and reorganised from the LDAK module family (nf-core naming, fixed
container/version/contract issues).
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