process CONTROLFREEC_FREEC { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) path fasta path fai path snp_position path known_snps path known_snps_tbi path chr_directory path mappability path target_bed path gccontent_profile output: tuple val(meta), path("*_ratio.BedGraph") , emit: bedgraph, optional: true tuple val(meta), path("*_control.cpn") , emit: control_cpn tuple val(meta), path("*_sample.cpn") , emit: sample_cpn tuple val(meta), path("GC_profile.*.cpn") , emit: gcprofile_cpn, optional:true tuple val(meta), path("*_BAF.txt") , emit: BAF tuple val(meta), path("*_CNVs") , emit: CNV tuple val(meta), path("*_info.txt") , emit: info tuple val(meta), path("*_ratio.txt") , emit: ratio tuple val(meta), path("config.txt") , emit: config path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: //"General" configurations def bedgraphoutput = task.ext.args?["general"]?["bedgraphoutput"] ? "BedGraphOutput = ${task.ext.args["general"]["bedgraphoutput"]}" : "" def chr_files = chr_directory ? "chrFiles =\${PWD}/${chr_directory}" : "" def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : "" def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : "" def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : "" def coefficientofvariation = task.ext.args?["general"]?["coefficientofvariation"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : "" def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : "" def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : "" def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : "" def forcegccontentnormalization = task.ext.args?["general"]?["forcegccontentnormalization"] ? "forceGCcontentNormalization = ${task.ext.args["general"]["forcegccontentnormalization"]}" : "" def gccontentprofile = gccontent_profile ? "GCcontentProfile = ${gccontent_profile}" : "" def mappability = mappability ? "gemMappabilityFile = \${PWD}/${mappability}" : "" def intercept = task.ext.args?["general"]?["intercept"] ? "intercept = ${task.ext.args["general"]["intercept"]}" : "" def mincnalength = task.ext.args?["general"]?["mincnalength"] ? "minCNAlength = ${task.ext.args["general"]["mincnalength"]}" : "" def minmappabilityperwindow = task.ext.args?["general"]?["minmappabilityperwindow"] ? "minMappabilityPerWindow = ${task.ext.args["general"]["minmappabilityperwindow"]}" : "" def minexpectedgc = task.ext.args?["general"]?["minexpectedgc"] ? "minExpectedGC = ${task.ext.args["general"]["minexpectedgc"]}" : "" def maxexpectedgc = task.ext.args?["general"]?["maxexpectedgc"] ? "maxExpectedGC = ${task.ext.args["general"]["maxexpectedgc"]}" : "" def minimalsubclonepresence = task.ext.args?["general"]?["minimalsubclonepresence"] ? "minimalSubclonePresence = ${task.ext.args["general"]["minimalsubclonepresence"]}" : "" def noisydata = task.ext.args?["general"]?["noisydata"] ? "noisyData = ${task.ext.args["general"]["noisydata"]}" : "" def output = task.ext.prefix ? "outputDir = \${PWD}/${task.ext.prefix}" : "" def ploidy = task.ext.args?["general"]?["ploidy"] ? "ploidy = ${task.ext.args["general"]["ploidy"]}" : "" def printNA = task.ext.args?["general"]?["printNA"] ? "printNA = ${task.ext.args["general"]["printNA"]}" : "" def readcountthreshold = task.ext.args?["general"]?["readcountthreshold"] ? "readCountThreshold = ${task.ext.args["general"]["readcountthreshold"]}" : "" def sex = task.ext.args?["general"]?["sex"] ? "sex = ${task.ext.args["general"]["sex"]}" : "" def step = task.ext.args?["general"]?["step"] ? "step = ${task.ext.args["general"]["step"]}" : "" def telocentromeric = task.ext.args?["general"]?["telocentromeric"] ? "telocentromeric = ${task.ext.args["general"]["telocentromeric"]} " : "" def uniquematch = task.ext.args?["general"]?["uniquematch"] ? "uniqueMatch = ${task.ext.args["general"]["uniquematch"]}" : "" def window = task.ext.args?["general"]?["window"] ? "window = ${task.ext.args["general"]["window"]}" : "" //"Control" configurations def matefile_normal = mpileup_normal ? "mateFile = \${PWD}/${mpileup_normal}" : "" def matecopynumberfile_normal = cpn_normal ? "mateCopyNumberFile = \${PWD}/${cpn_normal}" : "" def minipileup_normal = minipileup_normal ? "miniPileup = \${PWD}/${minipileup_normal}" : "" def inputformat_normal = task.ext.args?["control"]?["inputformat"] ? "inputFormat = ${task.ext.args["control"]["inputformat"]}" : "" def mateorientation_normal = task.ext.args?["control"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["control"]["mateorientation"]}" : "" //"Sample" configuration def matefile_tumor = mpileup_tumor ? "mateFile = \${PWD}/${mpileup_tumor}" : "" def matecopynumberfile_tumor = cpn_tumor ? "mateCopyNumberFile = \${PWD}/${cpn_tumor}" : "" def minipileup_tumor = minipileup_tumor ? "miniPileup = \${PWD}/${minipileup_tumor}" : "" def inputformat_tumor = task.ext.args?["sample"]?["inputformat"] ? "inputFormat = ${task.ext.args["sample"]["inputformat"]}" : "" def mateorientation_tumor = task.ext.args?["sample"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["sample"]["mateorientation"]}" : "" //"BAF" configuration def makepileup = snp_position ? "makePileup = \${PWD}/${snp_position}" : "" def fastafile = fasta ? "fastaFile = \${PWD}/${fasta}" : "" def minimalcoverageperposition = task.ext.args?["BAF"]?["minimalcoverageperposition"] ? "minimalCoveragePerPosition = ${task.ext.args["BAF"]["minimalcoverageperposition"]}" : "" def minimalqualityperposition = task.ext.args?["BAF"]?["minimalqualityperposition"] ? "minimalQualityPerPosition = ${task.ext.args["BAF"]["minimalqualityperposition"]}" : "" def shiftinquality = task.ext.args?["BAF"]?["shiftinquality"] ? "shiftInQuality = ${task.ext.args["BAF"]["shiftinquality"]}" : "" def snpfile = known_snps ? "SNPfile = \$PWD/${known_snps}" : "" //"Target" configuration def target_bed = target_bed ? "captureRegions = ${target_bed}" : "" """ touch config.txt echo "[general]" >> config.txt echo ${bedgraphoutput} >> config.txt echo ${breakpointthreshold} >> config.txt echo ${breakpointtype} >> config.txt echo ${chr_files} >> config.txt echo ${chr_length} >> config.txt echo ${coefficientofvariation} >> config.txt echo ${contamination} >> config.txt echo ${contaminationadjustment} >> config.txt echo ${degree} >> config.txt echo ${forcegccontentnormalization} >> config.txt echo ${gccontentprofile} >> config.txt echo ${mappability} >> config.txt echo ${intercept} >> config.txt echo ${mincnalength} >> config.txt echo ${minmappabilityperwindow} >> config.txt echo ${minexpectedgc} >> config.txt echo ${maxexpectedgc} >> config.txt echo ${minimalsubclonepresence} >> config.txt echo "maxThreads = ${task.cpus}" >> config.txt echo ${noisydata} >> config.txt echo ${output} >> config.txt echo ${ploidy} >> config.txt echo ${printNA} >> config.txt echo ${readcountthreshold} >> config.txt echo ${sex} >> config.txt echo ${step} >> config.txt echo ${telocentromeric} >> config.txt echo ${uniquematch} >> config.txt echo ${window} >> config.txt echo "[control]" >> config.txt echo ${matefile_normal} >> config.txt echo ${matecopynumberfile_normal} >> config.txt echo ${minipileup_normal} >> config.txt echo ${inputformat_normal} >> config.txt echo ${mateorientation_normal} >> config.txt echo "[sample]" >> config.txt echo ${matefile_tumor} >> config.txt echo ${matecopynumberfile_tumor} >> config.txt echo ${minipileup_tumor} >> config.txt echo ${inputformat_tumor} >> config.txt echo ${mateorientation_tumor} >> config.txt echo "[BAF]" >> config.txt echo ${makepileup} >> config.txt echo ${fastafile} >> config.txt echo ${minimalcoverageperposition} >> config.txt echo ${minimalqualityperposition} >> config.txt echo ${shiftinquality} >> config.txt echo ${snpfile} >> config.txt echo "[target]" >> config.txt echo ${target_bed} >> config.txt freec -conf config.txt cat <<-END_VERSIONS > versions.yml "${task.process}": controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" ) END_VERSIONS """ }