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e560fbbc3e
* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework. Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
60 lines
2.1 KiB
Text
60 lines
2.1 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process IMPUTEME_VCFTOPRS {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "YOUR-TOOL-HERE" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img"
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} else {
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container "biocontainers/imputeme:vv1.0.7_cv1"
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}
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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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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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#!/usr/bin/env Rscript
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#Set configuration - either from options.args or from defaults
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source("/imputeme/code/impute-me/functions.R")
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if(file.exists('$options.args')){
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set_conf("set_from_file",'$options.args')
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}else{
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set_conf("set_from_file", "/imputeme/code/impute-me/template/nextflow_default_configuration.R")
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}
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#main run
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return_message <- prepare_individual_genome('$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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