modules/gcta_calculateldscores

Calculate LD scores with GCTA and derive GREML-LDMS SNP groups

gctagenome-wide complex trait analysisld scorelinkage disequilibrium scoreldmslinkage disequilibrium and minor allele frequency stratificationgenetics

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

Description

Calculate LD scores with GCTA and derive GREML-LDMS SNP groups

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing PLINK1 genotype metadata e.g. [ id:'plink_simulated' ]

`bed`
`:file`

PLINK1 genotype primary file

*.{bed}

`bim`
`:file`

PLINK1 variant metadata file

*.{bim}

`fam`
`:file`

PLINK1 sample metadata file

*.{fam}

`ld_score_region`
`:integer`

LD-score region width passed to --ld-score-region. Callers should pass 200 for the default GCTA region width unless they are intentionally overriding it.

Output

name:type

description

pattern

`ld_scores`

`meta`
`:map`

Groovy Map containing PLINK1 genotype metadata e.g. [ id:'plink_simulated' ]

`*_gcta_ld.score.ld`
`:file`

GCTA LD score output file

*_gcta_ld.score.ld

`snp_group_files`

`meta`
`:map`

Groovy Map containing PLINK1 genotype metadata e.g. [ id:'plink_simulated' ]

`_snp_group.txt`
`:file`

LD-score SNP-group files for GCTA GREML-LDMS workflows

*_snp_group*.txt

`versions_gcta`

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

The process the versions were collected from

`gcta`
`:string`

The tool name

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

The command used to generate the version of the tool

`versions_rbase`

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

The process the versions were collected from

`r-base`
`:string`

The tool name

`Rscript -e "cat(as.character(getRversion()))"`
`:eval`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`gcta`
`:string`

The tool name

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

The command used to generate the version of the tool

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

The process the versions were collected from

`r-base`
`:string`

The tool name

`Rscript -e "cat(as.character(getRversion()))"`
`:eval`

The command used to generate the version of the tool

Tools

gcta
GPL-3.0-only

GCTA is a tool for genome-wide complex trait analysis.

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

modules/gcta_calculateldscores

Description

Input

`meta`
`:map`

`bed`
`:file`

`bim`
`:file`

`fam`
`:file`

`ld_score_region`
`:integer`

Output

`ld_scores`

`meta`
`:map`

`*_gcta_ld.score.ld`
`:file`

`snp_group_files`

`meta`
`:map`

`_snp_group.txt`
`:file`

`versions_gcta`

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

`gcta`
`:string`

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

`versions_rbase`

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

`r-base`
`:string`

`Rscript -e "cat(as.character(getRversion()))"`
`:eval`

Topics

`versions`

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

`gcta`
`:string`

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

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

`r-base`
`:string`

`Rscript -e "cat(as.character(getRversion()))"`
`:eval`

Tools

gcta
GPL-3.0-only

included in

maintainer

get in touch

modules/gcta_calculateldscores

Description

Input

meta :map

bed :file

bim :file

fam :file

ld_score_region :integer

Output

ld_scores

meta :map

*_gcta_ld.score.ld :file

snp_group_files

meta :map

*_snp_group*.txt :file

versions_gcta

${task.process} :string

gcta :string

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

versions_rbase

${task.process} :string

r-base :string

Rscript -e "cat(as.character(getRversion()))" :eval

Topics

versions

${task.process} :string

gcta :string

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

${task.process} :string

r-base :string

Rscript -e "cat(as.character(getRversion()))" :eval

Tools

gctaGPL-3.0-only

included in

maintainer

get in touch

`meta`
`:map`

`bed`
`:file`

`bim`
`:file`

`fam`
`:file`

`ld_score_region`
`:integer`

`ld_scores`

`meta`
`:map`

`*_gcta_ld.score.ld`
`:file`

`snp_group_files`

`meta`
`:map`

`_snp_group.txt`
`:file`

`versions_gcta`

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

`gcta`
`:string`

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

`versions_rbase`

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

`r-base`
`:string`

`Rscript -e "cat(as.character(getRversion()))"`
`:eval`

`versions`

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

`gcta`
`:string`

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

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

`r-base`
`:string`

`Rscript -e "cat(as.character(getRversion()))"`
`:eval`

gcta
GPL-3.0-only