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Add gcta/makebksparse module#11002

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lyh970817:modules/gcta-makebksparse-create
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Add gcta/makebksparse module#11002
lyh970817 wants to merge 3 commits into
nf-core:masterfrom
lyh970817:modules/gcta-makebksparse-create

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@lyh970817 lyh970817 commented Mar 21, 2026

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This PR adds the gcta/makebksparse module, which creates a sparse GRM for downstream fastGWA analyses.

This PR should merge after the gcta/makegrm module in #11650.

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  • This comment contains a description of changes (with reason).
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  • nf-core modules test gcta/makebksparse --profile docker
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@lyh970817 lyh970817 mentioned this pull request Mar 21, 2026
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@lyh970817 lyh970817 force-pushed the modules/gcta-makebksparse-create branch from cc1241a to 6e3cc10 Compare March 21, 2026 12:53
@lyh970817 lyh970817 mentioned this pull request Mar 21, 2026
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@lyh970817 lyh970817 force-pushed the modules/gcta-makebksparse-create branch 3 times, most recently from 40c1080 to b1b3cd2 Compare May 22, 2026 16:06
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Rationale for the meta rebinding at modules/nf-core/gcta/makebksparse/main.nf:L24:

The input meta.id identifies the dense GRM basename required by gcta --grm. makebksparse emits a new sparse GRM basename via --out ${prefix}_sp, and downstream consumers use that basename with --grm-sparse. Rebinding meta with meta + [id: "${prefix}_sp"] preserves any existing metadata while making the output tuple describe the emitted sparse GRM files rather than the dense input GRM.

The original dense basename is saved first as dense_prefix, so the command still consumes the dense GRM via --grm ${dense_prefix} while the emitted sparse_grm_files channel carries the sparse basename expected by downstream modules.

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