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nf-core_modules/modules/controlfreec/freec/main.nf

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controlfreec significance (#1451) * controlfreec significance * move freec files to own subfolder * Fix meta.yml naming * Fix meta.yml naming * Fix linting * Forgot to refactor * forgot more refactoring * Too much refactoring on output paths * Too little refactoring here * update checksum
2022-03-25 17:22:17 +00:00
process CONTROLFREEC_FREEC {
add controlfreec (#1333) * add drafty controlfreec * get sofatware version * use maps in map * update paths to new and soon-to-be merged test files, add more input docu * Stab at documenting args map * Update syntax * Bit more description * Make the linter happy * tests pass locally * Add outputs & docu * tests are failing locally now :/ but cpn file can also be added * All tests passing, need to update test data again to add folder * Clean up files * Clean up files * Clean up files * Don't know how to get the test to run with the direcotry for now. they pass locally though * Make linter happy * Name process back * Update to use tar folder * fix the checksum
2022-02-28 18:08:58 +00:00
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"]?["coefficient"] ? "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
"""
}
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