modules/gcta_bivariateremlldms

Run bivariate REML-LDMS analysis with an MGRM manifest

gctagenome-wide complex trait analysisremlrestricted maximum likelihoodbivariateldmslinkage disequilibrium and minor allele frequency stratificationgrmgenetic relationship matrixgenetics

https://github.com/nf-core/modules/[...]/modules/nf-core/gcta/bivariateremlldms

Description

Run bivariate REML-LDMS analysis with an MGRM manifest

Input

name:type

description

pattern

`meta`
`:map`

Groovy map containing MGRM metadata meta.id should match the MGRM manifest basename, for example plink_simulated_ldms for plink_simulated_ldms.mgrm

`mgrm_file`
`:file`

MGRM manifest file

*.mgrm

`grm_files`
`:file`

GRM bundles referenced by mgrm_file; each manifest entry should have matching *.grm.{id,bin,N.bin} files in this bundle

*.grm.*

`meta2`
`:map`

Groovy map containing phenotype file metadata for the same analysis unit as the primary MGRM metadata e.g. [ id:'plink_simulated_ldms' ]

`phenotype_file`
`:file`

Shared bivariate phenotype file passed to --pheno

*.{phe,pheno,txt,tsv}

`phenotype_col1`
`:integer`

First phenotype column passed to --reml-bivar (for example 1). Pass an empty value together with phenotype_col2 to use GCTA’s default bivariate phenotype columns.

`phenotype_col2`
`:integer`

Second phenotype column passed to --reml-bivar (for example 2). Pass an empty value together with phenotype_col1 to use GCTA’s default bivariate phenotype columns.

`meta3`
`:map`

Groovy map containing quantitative covariate metadata for the same analysis unit as the primary MGRM metadata e.g. [ id:'plink_simulated_ldms' ]

`quant_covariates_file`
`:file`

Quantitative covariates file, pass [] when absent

*.{covar,cov,txt,tsv}

`meta4`
`:map`

Groovy map containing categorical covariate metadata for the same analysis unit as the primary MGRM metadata e.g. [ id:'plink_simulated_ldms' ]

`cat_covariates_file`
`:file`

Categorical covariates file, pass [] when absent

*.{covar,cov,txt,tsv}

Output

name:type

description

pattern

`bivariate_results`

`meta`
`:map`

Groovy map containing MGRM metadata meta.id is used as the default output prefix

`*.hsq`
`:file`

Bivariate REML-LDMS result file

*.{hsq}

`log_file`

`meta`
`:map`

Groovy map containing MGRM metadata meta.id is used as the default output prefix

`*.log`
`:file`

Bivariate REML-LDMS log file

*.{log}

`versions_gcta`

`${task.process}`
`:string`

The process the version was collected from

`gcta`
`:string`

The tool name

`gcta --version | sed -En 's/^[] version v([0-9.]).*/\1/p'`
`:eval`

The command used to retrieve the GCTA version

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the version was collected from

`gcta`
`:string`

The tool name

`gcta --version | sed -En 's/^[] version v([0-9.]).*/\1/p'`
`:eval`

The command used to retrieve the GCTA version

Tools

gcta
GPL-3.0-only

Genome-wide Complex Trait Analysis (GCTA) estimates genetic relationships, variance components, and association statistics from genome-wide data.

yanglab.westlake.edu.cn/software/gcta yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf https://yanglab.westlake.edu.cn/software/gcta/

modules/gcta_bivariateremlldms

Description

Input

`meta`
`:map`

`mgrm_file`
`:file`

`grm_files`
`:file`

`meta2`
`:map`

`phenotype_file`
`:file`

`phenotype_col1`
`:integer`

`phenotype_col2`
`:integer`

`meta3`
`:map`

`quant_covariates_file`
`:file`

`meta4`
`:map`

`cat_covariates_file`
`:file`

Output

`bivariate_results`

`meta`
`:map`

`*.hsq`
`:file`

`log_file`

`meta`
`:map`

`*.log`
`:file`

`versions_gcta`

`${task.process}`
`:string`

`gcta`
`:string`

`gcta --version | sed -En 's/^[] version v([0-9.]).*/\1/p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gcta`
`:string`

`gcta --version | sed -En 's/^[] version v([0-9.]).*/\1/p'`
`:eval`

Tools

gcta
GPL-3.0-only

included in

maintainer

get in touch

modules/gcta_bivariateremlldms

Description

Input

meta :map

mgrm_file :file

grm_files :file

meta2 :map

phenotype_file :file

phenotype_col1 :integer

phenotype_col2 :integer

meta3 :map

quant_covariates_file :file

meta4 :map

cat_covariates_file :file

Output

bivariate_results

meta :map

*.hsq :file

log_file

meta :map

*.log :file

versions_gcta

${task.process} :string

gcta :string

gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\1/p' :eval

Topics

versions

${task.process} :string

gcta :string

gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\1/p' :eval

Tools

gctaGPL-3.0-only

included in

maintainer

get in touch

`meta`
`:map`

`mgrm_file`
`:file`

`grm_files`
`:file`

`meta2`
`:map`

`phenotype_file`
`:file`

`phenotype_col1`
`:integer`

`phenotype_col2`
`:integer`

`meta3`
`:map`

`quant_covariates_file`
`:file`

`meta4`
`:map`

`cat_covariates_file`
`:file`

`bivariate_results`

`meta`
`:map`

`*.hsq`
`:file`

`log_file`

`meta`
`:map`

`*.log`
`:file`

`versions_gcta`

`${task.process}`
`:string`

`gcta`
`:string`

`gcta --version | sed -En 's/^[] version v([0-9.]).*/\1/p'`
`:eval`

`versions`

`${task.process}`
`:string`

`gcta`
`:string`

`gcta --version | sed -En 's/^[] version v([0-9.]).*/\1/p'`
`:eval`

gcta
GPL-3.0-only