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Add gcta/fastgwa module
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‎modules/nf-core/gcta/fastgwa/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::gcta=1.94.1

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

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process GCTA_FASTGWA {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46b0d05f0daa47561d87d2a9cac5e51edc2c78e26f1bbab439c688386241a274/data'
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: 'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}"
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input:
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tuple val(meta), path(bed_pgen), path(bim_pvar), path(fam_psam)
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tuple val(meta2), path(sparse_grm_files)
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tuple val(meta3), path(phenotype_file)
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tuple val(meta4), path(quant_covariates_file)
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tuple val(meta5), path(cat_covariates_file)
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output:
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tuple val(meta), path("*.fastGWA"), emit: results
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tuple val(meta), path("*.log"), emit: log
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tuple val("${task.process}"), val("gcta"), eval("gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'"), emit: versions_gcta, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def genotype_suffix = bed_pgen.name.tokenize('.').last()
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def genotype_flag = genotype_suffix == 'pgen' ? '--pfile' : '--bfile'
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def genotype_prefix = bed_pgen.baseName
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def grm_arg = sparse_grm_files ? "--grm-sparse ${meta2.id}" : ''
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def qcovar_arg = quant_covariates_file ? "--qcovar ${quant_covariates_file}" : ''
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def covar_arg = cat_covariates_file ? "--covar ${cat_covariates_file}" : ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def out = prefix
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def extra_args = task.ext.args ?: ''
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"""
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set -euo pipefail
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gcta \\
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${genotype_flag} ${genotype_prefix} \\
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${grm_arg} \\
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--fastGWA-mlm \\
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--pheno ${phenotype_file} \\
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${qcovar_arg} \\
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${covar_arg} \\
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--thread-num ${task.cpus} \\
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--out ${out} ${extra_args}
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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def out = prefix
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"""
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touch ${out}.fastGWA
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touch ${out}.log
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"""
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}

‎modules/nf-core/gcta/fastgwa/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "gcta_fastgwa"
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description: Run GCTA fastGWA mixed linear model association analysis with PLINK genotype inputs
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keywords:
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- gcta
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- genome-wide complex trait analysis
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- fastgwa
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- fast genome-wide association
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- gwas
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- genome-wide association study
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- genetics
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tools:
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- "gcta":
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description: "Genome-wide Complex Trait Analysis (GCTA) estimates genetic relationships, variance components, and association statistics from genome-wide data."
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homepage: "https://yanglab.westlake.edu.cn/software/gcta/"
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documentation: "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf"
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tool_dev_url: "https://yanglab.westlake.edu.cn/software/gcta/"
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licence: ["GPL-3.0-only"]
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identifier: "biotools:gcta"
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input:
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- - meta:
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type: map
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description: |
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Groovy map containing PLINK genotype metadata
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e.g. `[ id:'plink_simulated' ]`
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- bed_pgen:
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type: file
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description: PLINK primary genotype file, either `.bed` or `.pgen`
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pattern: "*.{bed,pgen}"
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ontologies:
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- edam: "http://edamontology.org/format_3003"
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- bim_pvar:
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type: file
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description: PLINK sidecar file, either `.bim` or `.pvar`
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pattern: "*.{bim,pvar}"
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ontologies: []
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- fam_psam:
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type: file
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description: PLINK sidecar file, either `.fam` or `.psam`
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pattern: "*.{fam,psam}"
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ontologies: []
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- - meta2:
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type: map
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description: |
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Groovy map containing sparse GRM metadata
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e.g. `[ id:'plink_simulated_sp' ]`
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Used when sparse GRM files are supplied
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- sparse_grm_files:
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type: file
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description: Sparse GRM sidecar files, pass `[]` when absent
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pattern: "*.grm.{id,sp}"
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ontologies: []
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- - meta3:
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type: map
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description: |
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Groovy map containing phenotype metadata
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Keep only stable phenotype metadata in this map
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e.g. `[ id:'plink_simulated' ]`
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- phenotype_file:
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type: file
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description: Phenotype file
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pattern: "*.{phe,pheno,txt,tsv}"
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ontologies:
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- edam: "http://edamontology.org/format_3475"
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- - meta4:
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type: map
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description: |
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Groovy map containing quantitative covariate metadata
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e.g. `[ id:'covariates_quant' ]`
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- quant_covariates_file:
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type: file
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description: Quantitative covariates file, pass `[]` when absent
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pattern: "*.{covar,cov,txt,tsv}"
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ontologies:
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- edam: "http://edamontology.org/format_3475"
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- - meta5:
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type: map
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description: |
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Groovy map containing categorical covariate metadata
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e.g. `[ id:'covariates_cat' ]`
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- cat_covariates_file:
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type: file
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description: Categorical covariates file, pass `[]` when absent
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pattern: "*.{covar,cov,txt,tsv}"
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ontologies:
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- edam: "http://edamontology.org/format_3475"
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output:
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results:
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- - meta:
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type: map
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description: |
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Groovy map containing PLINK genotype metadata
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e.g. `[ id:'plink_simulated' ]`
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- "*.fastGWA":
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type: file
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description: FastGWA association results
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pattern: "*.fastGWA"
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ontologies:
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- edam: "http://edamontology.org/format_2330"
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log:
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- - meta:
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type: map
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description: |
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Groovy map containing PLINK genotype metadata
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e.g. `[ id:'plink_simulated' ]`
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- "*.log":
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type: file
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description: GCTA fastGWA log file
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pattern: "*.log"
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ontologies:
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- edam: "http://edamontology.org/format_2330"
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versions_gcta:
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- - "${task.process}":
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type: string
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description: The process the version was collected from
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- "gcta":
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type: string
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description: The tool name
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- "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
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type: eval
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description: The command used to retrieve the GCTA version
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The process the version was collected from
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- gcta:
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type: string
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description: The tool name
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- "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
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type: eval
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description: The command used to retrieve the GCTA version
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authors:
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- "@lyh970817"
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maintainers:
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- "@lyh970817"

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