#1934 Document and regenerate plink_simulated phenotype sidecars Pull request opened by lyh970817 PR checklist • I read the test-data specifications • I tried testing my module with available data and there is no compatible data in test-datasets • If I added data: I described the new files on the root

README.md

• If I modified data: I checked whether the root

README.md

is still up-to-date • I made sure to submit the smallest dataset possible (e.g. try .tar.gz for larger directories) Summary This draft PR is a follow-up to the earlier REGENIE test-datasets contribution in nf-core/test-datasets PR #1919. PR #1919 added the

plink_simulated

REGENIE phenotype and covariate sidecars, but it did not fully document those files in the repository metadata. This follow-up updates the root

README.md

, adds command-focused generation notes to

data/genomics/homo_sapiens/popgen/README.md

, and rewrites the REGENIE sidecars in a deterministic space-delimited form so the documented commands reproduce the checked-in files. Rationale The original REGENIE dataset PR is already closed and merged, so this needs to be submitted as a separate follow-up branch instead of amending the old submission. Opening a new PR keeps the corrective scope explicit: • document the existing

plink_simulated

phenotype-related files in the root inventory • record reproducible shell commands for generating

plink_simulated.phe

and the REGENIE sidecars in the

popgen

folder README • document that the

*_phenoname.phe

files use named phenotype columns (

Phenotype

,

QuantitativeTrait

,

BinaryTrait

) • align the checked-in REGENIE sidecar contents with those documented deterministic commands using space-delimited output to match the existing

plink_simulated.fam

/

plink_simulated.phe

style Additional documentation-only note This PR also documents the pre-existing

plink_simulated_phenoname.phe

file for completeness in the root inventory and

popgen

README. That file predates PR #1919 and is not being changed by this follow-up; its mention here is a pure documentation addition so the phenotype-file section is complete. Files touched •

README.md

•

data/genomics/homo_sapiens/popgen/README.md

•

data/genomics/homo_sapiens/popgen/plink_simulated_binary_phenoname.phe

•

data/genomics/homo_sapiens/popgen/plink_simulated_covariates.txt

•

data/genomics/homo_sapiens/popgen/plink_simulated_quantitative_phenoname.phe

Related PRs • Previous dataset PR: #1919 • Companion modules PR: nf-core/modules#10800 nf-core/test-datasets