mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
52 lines
1.7 KiB
Text
52 lines
1.7 KiB
Text
process IMPUTEME_VCFTOPRS {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "YOUR-TOOL-HERE" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img' :
|
|
'biocontainers/imputeme:vv1.0.7_cv1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf)
|
|
|
|
output:
|
|
tuple val(meta), path("*.json"), emit: json
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
#!/usr/bin/env Rscript
|
|
|
|
#Set configuration - either from args or from defaults
|
|
source("/imputeme/code/impute-me/functions.R")
|
|
if(file.exists('$args')){
|
|
set_conf("set_from_file",'$args')
|
|
}else{
|
|
set_conf("set_from_file", "/imputeme/code/impute-me/template/nextflow_default_configuration.R")
|
|
}
|
|
|
|
#main run
|
|
return_message <- prepare_individual_genome('$vcf',overrule_vcf_checks=T)
|
|
uniqueID <- sub(' </b>.+\$','',sub('^.+this run is <b> ','',return_message))
|
|
convert_vcfs_to_simple_format(uniqueID=uniqueID)
|
|
crawl_for_snps_to_analyze(uniqueIDs=uniqueID)
|
|
run_export_script(uniqueIDs=uniqueID)
|
|
file.copy(paste0("./",uniqueID,"/",uniqueID,"_data.json"),"output.json")
|
|
|
|
#version export. Have to hardcode process name and software name because
|
|
#won't run inside an R-block
|
|
version_file_path="versions.yml"
|
|
f <- file(version_file_path,"w")
|
|
writeLines("IMPUTEME_VCFTOPRS:", f)
|
|
writeLines(paste0(" imputeme: ", sub("^v","",get_conf("version"))),f)
|
|
close(f)
|
|
|
|
"""
|
|
|
|
}
|