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