Add GCTA modules by lyh970817 · Pull Request #10863 · nf-core/modules

lyh970817 · 2026-03-13T14:02:52Z

This PR upstreams 12 gcta modules for GRM construction and manipulation, REML and bivariate REML analyses, LDMS-based REML, LD-score calculation, and fastGWA. The companion shared-data PR is merged upstream: nf-core/test-datasets#1919

PR checklist

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Pull request overview

This PR upstreams a set of new gcta nf-core modules covering GRM construction/manipulation and REML / LDMS / LD-score / fastGWA workflows, including corresponding nf-test coverage and pinned software environments.

Changes:

Added 12 new modules/nf-core/gcta/* module implementations (main.nf) with containers/conda envs and topic: versions emission.
Added module metadata (meta.yml) and conda environments (environment.yml) for each module.
Added nf-test configs, tests, and snapshots for each new module.

Reviewed changes

Copilot reviewed 72 out of 72 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
modules/nf-core/gcta/addgrms/main.nf	New module process implementation for combining GRMs via MGRM.
modules/nf-core/gcta/addgrms/meta.yml	Module interface/IO metadata for `gcta_addgrms`.
modules/nf-core/gcta/addgrms/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/addgrms/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/addgrms/tests/main.nf.test	nf-test definitions for `gcta/addgrms`.
modules/nf-core/gcta/addgrms/tests/main.nf.test.snap	Snapshots for `gcta/addgrms` tests.
modules/nf-core/gcta/adjustgrm/main.nf	New module process implementation for GRM adjustment.
modules/nf-core/gcta/adjustgrm/meta.yml	Module interface/IO metadata for `gcta_adjustgrm`.
modules/nf-core/gcta/adjustgrm/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/adjustgrm/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/adjustgrm/tests/main.nf.test	nf-test definitions for `gcta/adjustgrm`.
modules/nf-core/gcta/adjustgrm/tests/main.nf.test.snap	Snapshots for `gcta/adjustgrm` tests.
modules/nf-core/gcta/bivariatereml/main.nf	New module process implementation for bivariate REML with dense GRM.
modules/nf-core/gcta/bivariatereml/meta.yml	Module interface/IO metadata for `gcta_bivariatereml`.
modules/nf-core/gcta/bivariatereml/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/bivariatereml/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/bivariatereml/tests/main.nf.test	nf-test definitions for `gcta/bivariatereml`.
modules/nf-core/gcta/bivariatereml/tests/main.nf.test.snap	Snapshots for `gcta/bivariatereml` tests.
modules/nf-core/gcta/bivariateremlldms/main.nf	New module process implementation for bivariate REML-LDMS with MGRM.
modules/nf-core/gcta/bivariateremlldms/meta.yml	Module interface/IO metadata for `gcta_bivariateremlldms`.
modules/nf-core/gcta/bivariateremlldms/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/bivariateremlldms/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/bivariateremlldms/tests/main.nf.test	nf-test definitions for `gcta/bivariateremlldms`.
modules/nf-core/gcta/bivariateremlldms/tests/main.nf.test.snap	Snapshots for `gcta/bivariateremlldms` tests.
modules/nf-core/gcta/calculateldscores/main.nf	New module process implementation for LD-score calculation + SNP grouping.
modules/nf-core/gcta/calculateldscores/meta.yml	Module interface/IO metadata for `gcta_calculateldscores`.
modules/nf-core/gcta/calculateldscores/environment.yml	Conda environment pinning `gcta` + `r-base`.
modules/nf-core/gcta/calculateldscores/tests/nextflow.config	Test config (incl. CPU override) + test-datasets base path.
modules/nf-core/gcta/calculateldscores/tests/main.nf.test	nf-test definitions for `gcta/calculateldscores`.
modules/nf-core/gcta/calculateldscores/tests/main.nf.test.snap	Snapshots for `gcta/calculateldscores` tests.
modules/nf-core/gcta/fastgwa/main.nf	New module process implementation for GCTA fastGWA (MLM/LR).
modules/nf-core/gcta/fastgwa/meta.yml	Module interface/IO metadata for `gcta_fastgwa`.
modules/nf-core/gcta/fastgwa/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/fastgwa/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/fastgwa/tests/main.nf.test	nf-test definitions for `gcta/fastgwa`.
modules/nf-core/gcta/fastgwa/tests/main.nf.test.snap	Snapshots for `gcta/fastgwa` tests.
modules/nf-core/gcta/filtergrmwithkeep/main.nf	New module process implementation for filtering GRM using keep file.
modules/nf-core/gcta/filtergrmwithkeep/meta.yml	Module interface/IO metadata for `gcta_filtergrmwithkeep`.
modules/nf-core/gcta/filtergrmwithkeep/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/filtergrmwithkeep/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/filtergrmwithkeep/tests/main.nf.test	nf-test definitions for `gcta/filtergrmwithkeep`.
modules/nf-core/gcta/filtergrmwithkeep/tests/main.nf.test.snap	Snapshots for `gcta/filtergrmwithkeep` tests.
modules/nf-core/gcta/makebksparse/main.nf	New module process implementation for converting dense GRM to sparse GRM.
modules/nf-core/gcta/makebksparse/meta.yml	Module interface/IO metadata for `gcta_makebksparse`.
modules/nf-core/gcta/makebksparse/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/makebksparse/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/makebksparse/tests/main.nf.test	nf-test definitions for `gcta/makebksparse`.
modules/nf-core/gcta/makebksparse/tests/main.nf.test.snap	Snapshots for `gcta/makebksparse` tests.
modules/nf-core/gcta/makegrmpart/main.nf	New module process implementation for GRM partition construction.
modules/nf-core/gcta/makegrmpart/meta.yml	Module interface/IO metadata for `gcta_makegrmpart`.
modules/nf-core/gcta/makegrmpart/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/makegrmpart/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/makegrmpart/tests/main.nf.test	nf-test definitions for `gcta/makegrmpart`.
modules/nf-core/gcta/makegrmpart/tests/main.nf.test.snap	Snapshots for `gcta/makegrmpart` tests.
modules/nf-core/gcta/reml/main.nf	New module process implementation for univariate REML with dense GRM.
modules/nf-core/gcta/reml/meta.yml	Module interface/IO metadata for `gcta_reml`.
modules/nf-core/gcta/reml/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/reml/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/reml/tests/main.nf.test	nf-test definitions for `gcta/reml`.
modules/nf-core/gcta/reml/tests/main.nf.test.snap	Snapshots for `gcta/reml` tests.
modules/nf-core/gcta/remlldms/main.nf	New module process implementation for REML-LDMS with MGRM.
modules/nf-core/gcta/remlldms/meta.yml	Module interface/IO metadata for `gcta_remlldms`.
modules/nf-core/gcta/remlldms/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/remlldms/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/remlldms/tests/main.nf.test	nf-test definitions for `gcta/remlldms`.
modules/nf-core/gcta/remlldms/tests/main.nf.test.snap	Snapshots for `gcta/remlldms` tests.
modules/nf-core/gcta/removerelatedsubjects/main.nf	New module process implementation for removing related subjects (GRM cutoff).
modules/nf-core/gcta/removerelatedsubjects/meta.yml	Module interface/IO metadata for `gcta_removerelatedsubjects`.
modules/nf-core/gcta/removerelatedsubjects/environment.yml	Conda environment pinning `gcta`.
modules/nf-core/gcta/removerelatedsubjects/tests/nextflow.config	Test config wiring test-datasets base path.
modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test	nf-test definitions for `gcta/removerelatedsubjects`.
modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test.snap	Snapshots for `gcta/removerelatedsubjects` tests.

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modules/nf-core/gcta/bivariateremlldms/main.nf

+    output:
+    tuple val(meta), path("${meta.id}.hsq"), emit: bivariate_results
+    tuple val(meta), path("${meta.id}.log"), emit: log_file
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/calculateldscores/main.nf

+    output:
+    tuple val(meta), path("${meta.id}_gcta_ld.score.ld"), emit: ld_scores
+    tuple val(meta), path("${meta.id}_snp_group1.txt"), path("${meta.id}_snp_group2.txt"), path("${meta.id}_snp_group3.txt"), path("${meta.id}_snp_group4.txt"), emit: snp_group_files
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/reml/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}.hsq"), emit: reml_results
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/remlldms/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}.hsq"), emit: reml_results
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/addgrms/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}.grm.id"), path("${meta.id}.grm.bin"), path("${meta.id}.grm.N.bin"), emit: combined_grm
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/filtergrmwithkeep/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}_unrel.grm.id"), path("${meta.id}_unrel.grm.bin"), path("${meta.id}_unrel.grm.N.bin"), emit: filtered_grm
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/makebksparse/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}_sp.grm.id"), path("${meta.id}_sp.grm.sp"), emit: sparse_grm_files
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/makegrmpart/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}.part_${meta.nparts_gcta}_${meta.part_gcta_job}.grm.id"), path("${meta.id}.part_${meta.nparts_gcta}_${meta.part_gcta_job}.grm.bin"), path("${meta.id}.part_${meta.nparts_gcta}_${meta.part_gcta_job}.grm.N.bin"), emit: grm_files
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/removerelatedsubjects/main.nf

+    output:
+    tuple val(meta), path("${meta.id}_unrel05.grm.id"), path("${meta.id}_unrel05.grm.bin"), path("${meta.id}_unrel05.grm.N.bin"), emit: grm_files
+    tuple val(meta), path("${meta.id}_unrel05.grm.id"), emit: keep_file
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


modules/nf-core/gcta/adjustgrm/main.nf

+
+    output:
+    tuple val(meta), path("${meta.id}_adj.grm.id"), path("${meta.id}_adj.grm.bin"), path("${meta.id}_adj.grm.N.bin"), emit: grm_files
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | head -n 1"), emit: versions_gcta, topic: versions


famosab

Please split this PR into multiple PRs, one per module

lyh970817 · 2026-03-20T10:21:45Z

Please split this PR into multiple PRs, one per module

Thanks for reviewing. I'll close this one and open PRs for each module.

lyh970817 · 2026-03-21T09:54:28Z

Superseded by the split module PRs:

famosab · 2026-03-24T08:32:39Z

you can post the individual PRs in the #request-review channel in slack and you will most likely find someone to review them step by step :)

lyh970817 mentioned this pull request Mar 13, 2026

Add nf-core GCTA modules nf-core/gwas#80

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lyh970817 marked this pull request as draft March 13, 2026 15:07

lyh970817 marked this pull request as ready for review March 14, 2026 07:48

lyh970817 requested a review from Copilot March 14, 2026 15:32

Copilot started reviewing on behalf of lyh970817 March 14, 2026 15:32 View session

Copilot AI reviewed Mar 14, 2026

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lyh970817 added 9 commits March 19, 2026 01:20

feat: add gcta modules

71fda52

test: reuse shared datasets in gcta module tests

d84b94f

feat: refine gcta modules and tests

689f6e9

test: stabilize gcta bivariateremlldms snapshot

f1d8361

fix: capture gcta versions correctly

09e8a36

Add mpheno support to GCTA REML modules

d8b481e

Add explicit grm-adj input to GCTA ADJUSTGRM

3e5cfbc

fix: use valid meta schema type for gcta adjustgrm grm_adj

d92f6dc

Update GCTA snapshots for refreshed popgen fixtures

e6f5122

lyh970817 force-pushed the modules/gcta-create branch from 9b232f6 to e6f5122 Compare March 18, 2026 17:20

lyh970817 marked this pull request as draft March 18, 2026 17:21

lyh970817 marked this pull request as ready for review March 19, 2026 04:23

famosab requested changes Mar 19, 2026

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lyh970817 closed this Mar 21, 2026

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Add GCTA modules#10863

Add GCTA modules#10863
lyh970817 wants to merge 9 commits intonf-core:masterfrom
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lyh970817 commented Mar 13, 2026 •

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