#1919 Add REGENIE phenotype and covariate sidecars for plink_simulated Pull request opened by lyh970817 Summary This PR adds three tiny

plink_simulated_*

sidecar files to

data/genomics/homo_sapiens/popgen/

so REGENIE module tests can cover: • quantitative phenotype input • binary phenotype input in REGENIE-compatible

0/1

form • explicit covariate input The new files extend the existing

plink_simulated

cohort rather than introducing a second GWAS fixture set. Files Added •

data/genomics/homo_sapiens/popgen/plink_simulated_quantitative_phenoname.phe

•

data/genomics/homo_sapiens/popgen/plink_simulated_binary_phenoname.phe

•

data/genomics/homo_sapiens/popgen/plink_simulated_covariates.txt

Rationale

nf-core/modules

already reuses

plink_simulated.{bed,bim,fam,pgen,pvar,psam}

for GWAS/popgen tests, but the existing phenotype sidecars are not sufficient to exercise REGENIE's intended test matrix cleanly: • the existing

plink_simulated_phenoname.phe

is a binary

1/2

phenotype file, not a continuous quantitative trait • that existing file was only usable for the quantitative path via a

--force-qt

workaround • REGENIE binary mode expects

0/1/NA

, so a dedicated

0/1

binary sidecar is also needed • there was no shared covariate sidecar for the same cohort Adding small deterministic sidecars on top of the existing cohort keeps the dataset reusable and avoids duplicating genotype bundles. Data Provenance These files are deterministic sidecars derived from the sample identifiers in the existing

plink_simulated

dataset. They are synthetic tabular fixtures only: • no sensitive or controlled-access data • no external downloads • no new biological source material Size The added files are small: • `plink_simulated_quantitative_phenoname.phe`: 4.5 KB • `plink_simulated_binary_phenoname.phe`: 3.0 KB • `plink_simulated_covariates.txt`: 7.4 KB Total added footprint: about 15 KB. Validation These files were validated locally by pointing the companion

nf-core/modules

REGENIE tests at this branch and running: NF_MODULES_TESTDATA_BASE_PATH='file:///.../test-datasets-work/data/' nf-test test modules/nf-core/regenie/step1/tests/main.nf.test --profile singularity --updateSnapshot --verbose --stopOnFirstFailure NF_MODULES_TESTDATA_BASE_PATH='file:///.../test-datasets-work/data/' nf-test test modules/nf-core/regenie/step2/tests/main.nf.test --profile singularity --updateSnapshot --verbose --stopOnFirstFailure Companion PR This dataset PR is required by the companion

nf-core/modules

PR: nf-core/modules#10800 nf-core/test-datasets