mirror of
https://github.com/MillironX/nf-core_modules.git
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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
This commit is contained in:
FriederikeHanssen
GitHub
parent
38ffbfdb63
commit
c189835b1b
7 changed files with 436 additions and 1 deletions
158
modules/controlfreec/main.nf
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158
modules/controlfreec/main.nf
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process CONTROLFREEC {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
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'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
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input:
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tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)
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path fasta
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path fai
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path snp_position
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path known_snps
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path known_snps_tbi
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path chr_directory
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path mappability
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path target_bed
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path gccontent_profile
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output:
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tuple val(meta), path("*_ratio.BedGraph") , emit: bedgraph, optional: true
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tuple val(meta), path("*_control.cpn") , emit: control_cpn
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tuple val(meta), path("*_sample.cpn") , emit: sample_cpn
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tuple val(meta), path("GC_profile.*.cpn") , emit: gcprofile_cpn, optional:true
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tuple val(meta), path("*_BAF.txt") , emit: BAF
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tuple val(meta), path("*_CNVs") , emit: CNV
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tuple val(meta), path("*_info.txt") , emit: info
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tuple val(meta), path("*_ratio.txt") , emit: ratio
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tuple val(meta), path("config.txt") , emit: config
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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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//"General" configurations
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def bedgraphoutput = task.ext.args?["general"]?["bedgraphoutput"] ? "BedGraphOutput = ${task.ext.args["general"]["bedgraphoutput"]}" : ""
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def chr_files = chr_directory ? "chrFiles =\${PWD}/${chr_directory}" : ""
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def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : ""
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def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : ""
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def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : ""
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def coefficientofvariation = task.ext.args?["general"]?["coefficient"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : ""
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def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : ""
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def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : ""
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def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : ""
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def forcegccontentnormalization = task.ext.args?["general"]?["forcegccontentnormalization"] ? "forceGCcontentNormalization = ${task.ext.args["general"]["forcegccontentnormalization"]}" : ""
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def gccontentprofile = gccontent_profile ? "GCcontentProfile = ${gccontent_profile}" : ""
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def mappability = mappability ? "gemMappabilityFile = \${PWD}/${mappability}" : ""
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def intercept = task.ext.args?["general"]?["intercept"] ? "intercept = ${task.ext.args["general"]["intercept"]}" : ""
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def mincnalength = task.ext.args?["general"]?["mincnalength"] ? "minCNAlength = ${task.ext.args["general"]["mincnalength"]}" : ""
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def minmappabilityperwindow = task.ext.args?["general"]?["minmappabilityperwindow"] ? "minMappabilityPerWindow = ${task.ext.args["general"]["minmappabilityperwindow"]}" : ""
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def minexpectedgc = task.ext.args?["general"]?["minexpectedgc"] ? "minExpectedGC = ${task.ext.args["general"]["minexpectedgc"]}" : ""
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def maxexpectedgc = task.ext.args?["general"]?["maxexpectedgc"] ? "maxExpectedGC = ${task.ext.args["general"]["maxexpectedgc"]}" : ""
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def minimalsubclonepresence = task.ext.args?["general"]?["minimalsubclonepresence"] ? "minimalSubclonePresence = ${task.ext.args["general"]["minimalsubclonepresence"]}" : ""
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def noisydata = task.ext.args?["general"]?["noisydata"] ? "noisyData = ${task.ext.args["general"]["noisydata"]}" : ""
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def output = task.ext.prefix ? "outputDir = \${PWD}/${task.ext.prefix}" : ""
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def ploidy = task.ext.args?["general"]?["ploidy"] ? "ploidy = ${task.ext.args["general"]["ploidy"]}" : ""
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def printNA = task.ext.args?["general"]?["printNA"] ? "printNA = ${task.ext.args["general"]["printNA"]}" : ""
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def readcountthreshold = task.ext.args?["general"]?["readcountthreshold"] ? "readCountThreshold = ${task.ext.args["general"]["readcountthreshold"]}" : ""
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def sex = task.ext.args?["general"]?["sex"] ? "sex = ${task.ext.args["general"]["sex"]}" : ""
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def step = task.ext.args?["general"]?["step"] ? "step = ${task.ext.args["general"]["step"]}" : ""
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def telocentromeric = task.ext.args?["general"]?["telocentromeric"] ? "telocentromeric = ${task.ext.args["general"]["telocentromeric"]} " : ""
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def uniquematch = task.ext.args?["general"]?["uniquematch"] ? "uniqueMatch = ${task.ext.args["general"]["uniquematch"]}" : ""
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def window = task.ext.args?["general"]?["window"] ? "window = ${task.ext.args["general"]["window"]}" : ""
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//"Control" configurations
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def matefile_normal = mpileup_normal ? "mateFile = \${PWD}/${mpileup_normal}" : ""
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def matecopynumberfile_normal = cpn_normal ? "mateCopyNumberFile = \${PWD}/${cpn_normal}" : ""
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def minipileup_normal = minipileup_normal ? "miniPileup = \${PWD}/${minipileup_normal}" : ""
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def inputformat_normal = task.ext.args?["control"]?["inputformat"] ? "inputFormat = ${task.ext.args["control"]["inputformat"]}" : ""
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def mateorientation_normal = task.ext.args?["control"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["control"]["mateorientation"]}" : ""
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//"Sample" configuration
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def matefile_tumor = mpileup_tumor ? "mateFile = \${PWD}/${mpileup_tumor}" : ""
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def matecopynumberfile_tumor = cpn_tumor ? "mateCopyNumberFile = \${PWD}/${cpn_tumor}" : ""
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def minipileup_tumor = minipileup_tumor ? "miniPileup = \${PWD}/${minipileup_tumor}" : ""
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def inputformat_tumor = task.ext.args?["sample"]?["inputformat"] ? "inputFormat = ${task.ext.args["sample"]["inputformat"]}" : ""
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def mateorientation_tumor = task.ext.args?["sample"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["sample"]["mateorientation"]}" : ""
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//"BAF" configuration
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def makepileup = snp_position ? "makePileup = \${PWD}/${snp_position}" : ""
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def fastafile = fasta ? "fastaFile = \${PWD}/${fasta}" : ""
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def minimalcoverageperposition = task.ext.args?["BAF"]?["minimalcoverageperposition"] ? "minimalCoveragePerPosition = ${task.ext.args["BAF"]["minimalcoverageperposition"]}" : ""
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def minimalqualityperposition = task.ext.args?["BAF"]?["minimalqualityperposition"] ? "minimalQualityPerPosition = ${task.ext.args["BAF"]["minimalqualityperposition"]}" : ""
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def shiftinquality = task.ext.args?["BAF"]?["shiftinquality"] ? "shiftInQuality = ${task.ext.args["BAF"]["shiftinquality"]}" : ""
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def snpfile = known_snps ? "SNPfile = \$PWD/${known_snps}" : ""
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//"Target" configuration
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def target_bed = target_bed ? "captureRegions = ${target_bed}" : ""
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"""
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touch config.txt
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echo "[general]" >> config.txt
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echo ${bedgraphoutput} >> config.txt
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echo ${breakpointthreshold} >> config.txt
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echo ${breakpointtype} >> config.txt
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echo ${chr_files} >> config.txt
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echo ${chr_length} >> config.txt
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echo ${coefficientofvariation} >> config.txt
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echo ${contamination} >> config.txt
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echo ${contaminationadjustment} >> config.txt
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echo ${degree} >> config.txt
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echo ${forcegccontentnormalization} >> config.txt
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echo ${gccontentprofile} >> config.txt
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echo ${mappability} >> config.txt
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echo ${intercept} >> config.txt
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echo ${mincnalength} >> config.txt
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echo ${minmappabilityperwindow} >> config.txt
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echo ${minexpectedgc} >> config.txt
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echo ${maxexpectedgc} >> config.txt
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echo ${minimalsubclonepresence} >> config.txt
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echo "maxThreads = ${task.cpus}" >> config.txt
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echo ${noisydata} >> config.txt
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echo ${output} >> config.txt
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echo ${ploidy} >> config.txt
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echo ${printNA} >> config.txt
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echo ${readcountthreshold} >> config.txt
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echo ${sex} >> config.txt
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echo ${step} >> config.txt
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echo ${telocentromeric} >> config.txt
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echo ${uniquematch} >> config.txt
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echo ${window} >> config.txt
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echo "[control]" >> config.txt
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echo ${matefile_normal} >> config.txt
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echo ${matecopynumberfile_normal} >> config.txt
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echo ${minipileup_normal} >> config.txt
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echo ${inputformat_normal} >> config.txt
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echo ${mateorientation_normal} >> config.txt
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echo "[sample]" >> config.txt
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echo ${matefile_tumor} >> config.txt
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echo ${matecopynumberfile_tumor} >> config.txt
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echo ${minipileup_tumor} >> config.txt
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echo ${inputformat_tumor} >> config.txt
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echo ${mateorientation_tumor} >> config.txt
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echo "[BAF]" >> config.txt
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echo ${makepileup} >> config.txt
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echo ${fastafile} >> config.txt
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echo ${minimalcoverageperposition} >> config.txt
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echo ${minimalqualityperposition} >> config.txt
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echo ${shiftinquality} >> config.txt
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echo ${snpfile} >> config.txt
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echo "[target]" >> config.txt
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echo ${target_bed} >> config.txt
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freec -conf config.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
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END_VERSIONS
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"""
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}
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183
modules/controlfreec/meta.yml
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183
modules/controlfreec/meta.yml
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name: controlfreec
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description: Copy number and genotype annotation from whole genome and whole exome sequencing data
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keywords:
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- cna
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- cnv
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- somatic
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- single
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- tumor-only
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tools:
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- controlfreec:
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description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
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homepage: http://boevalab.inf.ethz.ch/FREEC
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documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
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tool_dev_url: https://github.com/BoevaLab/FREEC/
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doi: "10.1093/bioinformatics/btq635"
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licence: ['GPL >=2']
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input:
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- args:
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type: map
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description: |
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Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
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<optional> parameters can be removed from the map, if they are not set. All value must be surrounded by quotes, meta map parameters can be set with, i.e. sex = meta.sex:
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For default values, please check the documentation above.
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```
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{
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[
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"general" :[
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"bedgraphoutput": <optional>,
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"breakpointthreshold": <optional>,
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"breakpointtype": <optional>,
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"coefficientofvariation": <optional>,
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"contamination": <optional>,
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"contaminationadjustment": <optional>,
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"degree": <optional>,
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"forcegccontentnormalization": <optional>,
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"gccontentprofile": <optional>,
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"intercept": <optional>,
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"mincnalength": <optional>,
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"minmappabilityperwindow": <optional>,
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"minexpectedgc": <optional>,
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"maxexpectedgc": <optional>,
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"minimalsubclonepresence": <optional>,
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"noisydata": <optional>,
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"ploidy": <optional>,
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"printNA": <optional>,
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"readcountthreshold": <optional >,
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"sex": <optional>,
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"step": <optional value>,
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"telocentromeric": <optional>,
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"uniquematch": <optional>,
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"window": <optional>
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],
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"control":[
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"inputformat": <required>,
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"mateorientation": <optional>,
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],
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"sample":[
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"inputformat": <required>,
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"mateorientation": <optional>,
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],
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"BAF":[
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"minimalcoverageperposition": <optional>,
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"minimalqualityperposition": <optional>,
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"shiftinquality": <optional>
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]
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]
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}
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```
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- mateFile_normal:
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type: file
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description: File with mapped reads
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pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
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- mateFile_tumor:
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type: file
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description: File with mapped reads
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pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
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- cpn_normal:
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type: file
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description: Raw copy number profiles (optional)
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pattern: "*.cpn"
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- cpn_tumor:
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type: file
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description: Raw copy number profiles (optional)
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pattern: "*.cpn"
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- minipileup_normal:
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type: file
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description: miniPileup file from previous run (optional)
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pattern: "*.pileup"
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- minipileup_tumor:
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type: file
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description: miniPileup file from previous run (optional)
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pattern: "*.pileup"
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- fasta:
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type: file
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description: Reference file (optional; required if args 'makePileup' is set)
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pattern: "*.{fasta,fna,fa}"
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- fai:
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type: file
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description: Fasta index
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pattern: "*.fai"
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- snp_position:
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type: file
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description:
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pattern: "*.{}"
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- known_snps:
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type: file
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description: File with known SNPs
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pattern: "*.{vcf,vcf.gz}"
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- known_snps_tbi:
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type: file
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description: Index of known_snps
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pattern: "*.tbi"
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- chr_directory:
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type: file
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description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)
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pattern: "*/"
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- mappability:
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type: file
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description: Contains information of mappable positions (optional)
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pattern: "*.gem"
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- target_bed:
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type: file
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description: Sorted bed file containing capture regions (optional)
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pattern: "*.bed"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- bedgraph:
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type: file
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||||||
|
description: Bedgraph format for the UCSC genome browser
|
||||||
|
pattern: ".bedgraph"
|
||||||
|
- control_cpn:
|
||||||
|
type: file
|
||||||
|
description: files with raw copy number profiles
|
||||||
|
pattern: "*_control.cpn"
|
||||||
|
- sample_cpn:
|
||||||
|
type: file
|
||||||
|
description: files with raw copy number profiles
|
||||||
|
pattern: "*_sample.cpn"
|
||||||
|
- gcprofile_cpn:
|
||||||
|
type: file
|
||||||
|
description: file with GC-content profile.
|
||||||
|
pattern: "GC_profile.*.cpn"
|
||||||
|
- BAF:
|
||||||
|
type: file
|
||||||
|
description: file B-allele frequencies for each possibly heterozygous SNP position
|
||||||
|
pattern: "*_BAF.txt"
|
||||||
|
- CNV:
|
||||||
|
type: file
|
||||||
|
description: file with coordinates of predicted copy number alterations.
|
||||||
|
pattern: "*_CNVs"
|
||||||
|
- info:
|
||||||
|
type: file
|
||||||
|
description: parsable file with information about FREEC run
|
||||||
|
pattern: "*_info.txt"
|
||||||
|
- ratio:
|
||||||
|
type: file
|
||||||
|
description: file with ratios and predicted copy number alterations for each window
|
||||||
|
pattern: "*_ratio.txt"
|
||||||
|
- config:
|
||||||
|
type: file
|
||||||
|
description: Config file used to run Control-FREEC
|
||||||
|
pattern: "config.txt"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@FriederikeHanssen"
|
||||||
|
|
@ -356,6 +356,10 @@ cnvkit/batch:
|
||||||
- modules/cnvkit/batch/**
|
- modules/cnvkit/batch/**
|
||||||
- tests/modules/cnvkit/batch/**
|
- tests/modules/cnvkit/batch/**
|
||||||
|
|
||||||
|
controlfreec:
|
||||||
|
- modules/controlfreec/**
|
||||||
|
- tests/modules/controlfreec/**
|
||||||
|
|
||||||
cooler/cload:
|
cooler/cload:
|
||||||
- modules/cooler/cload/**
|
- modules/cooler/cload/**
|
||||||
- tests/modules/cooler/cload/**
|
- tests/modules/cooler/cload/**
|
||||||
|
|
|
||||||
|
|
@ -123,10 +123,12 @@ params {
|
||||||
genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
|
genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
|
||||||
genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
|
genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
|
||||||
genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
|
genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
|
||||||
|
genome_21_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
|
||||||
genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
|
genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
|
||||||
genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
|
genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
|
||||||
genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
|
genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
|
||||||
genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
|
genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
|
||||||
|
genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
|
||||||
|
|
||||||
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
|
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
|
||||||
dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
|
dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
|
||||||
|
|
@ -272,6 +274,9 @@ params {
|
||||||
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
||||||
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
||||||
|
|
||||||
|
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
|
||||||
|
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
|
||||||
|
|
||||||
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
||||||
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
||||||
|
|
||||||
|
|
|
||||||
37
tests/modules/controlfreec/main.nf
Normal file
37
tests/modules/controlfreec/main.nf
Normal file
|
|
@ -0,0 +1,37 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
|
||||||
|
include { UNTAR } from '../../../modules/untar/main.nf'
|
||||||
|
workflow test_controlfreec {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false, sex:'XX' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
|
||||||
|
[],[],[],[]
|
||||||
|
]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||||
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||||
|
|
||||||
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
|
||||||
|
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
|
||||||
|
|
||||||
|
chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
|
||||||
|
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR(chrfiles)
|
||||||
|
CONTROLFREEC ( input,
|
||||||
|
fasta,
|
||||||
|
fai,
|
||||||
|
[],
|
||||||
|
dbsnp,
|
||||||
|
dbsnp_tbi,
|
||||||
|
UNTAR.out.untar,
|
||||||
|
[],
|
||||||
|
target_bed,
|
||||||
|
[]
|
||||||
|
)
|
||||||
|
}
|
||||||
26
tests/modules/controlfreec/nextflow.config
Normal file
26
tests/modules/controlfreec/nextflow.config
Normal file
|
|
@ -0,0 +1,26 @@
|
||||||
|
process {
|
||||||
|
|
||||||
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||||
|
|
||||||
|
withName:CONTROLFREEC{
|
||||||
|
ext.args = { [
|
||||||
|
"sample":[
|
||||||
|
inputformat: 'pileup',
|
||||||
|
mateorientation: 'FR'
|
||||||
|
],
|
||||||
|
"general" :[
|
||||||
|
bedgraphoutput: "TRUE",
|
||||||
|
noisydata: "TRUE",
|
||||||
|
minexpectedgc: "0",
|
||||||
|
readcountthreshold: "1",
|
||||||
|
sex: meta.sex,
|
||||||
|
window: "10",
|
||||||
|
],
|
||||||
|
"control":[
|
||||||
|
inputformat: "pileup",
|
||||||
|
mateorientation: "FR"
|
||||||
|
]
|
||||||
|
]
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
22
tests/modules/controlfreec/test.yml
Normal file
22
tests/modules/controlfreec/test.yml
Normal file
|
|
@ -0,0 +1,22 @@
|
||||||
|
- name: controlfreec test_controlfreec
|
||||||
|
command: nextflow run tests/modules/controlfreec -entry test_controlfreec -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- controlfreec
|
||||||
|
files:
|
||||||
|
- path: output/controlfreec/config.txt
|
||||||
|
- path: output/controlfreec/test.mpileup.gz_control.cpn
|
||||||
|
md5sum: 1768b571677c418560e5a8fe203bdc79
|
||||||
|
- path: output/controlfreec/test2.mpileup.gz_BAF.txt
|
||||||
|
md5sum: 3bb7437001cf061a77eaf87b8558c48d
|
||||||
|
- path: output/controlfreec/test2.mpileup.gz_CNVs
|
||||||
|
md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
|
||||||
|
- path: output/controlfreec/test2.mpileup.gz_info.txt
|
||||||
|
md5sum: 1a3055d35028525ccc9e693cc9f335e0
|
||||||
|
- path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
|
||||||
|
md5sum: 8ba455b232be20cdcc5bf1e4035e8032
|
||||||
|
- path: output/controlfreec/test2.mpileup.gz_ratio.txt
|
||||||
|
md5sum: b76b2434de710325069e37fb1e132760
|
||||||
|
- path: output/controlfreec/test2.mpileup.gz_sample.cpn
|
||||||
|
md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
|
||||||
|
- path: output/controlfreec/versions.yml
|
||||||
|
md5sum: ff93f6466d4686aab708425782c6c848
|
||||||
Loading…
Reference in a new issue