From c189835b1bb444e5ee87416fdbea66e2c2ba365e Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 28 Feb 2022 19:08:58 +0100 Subject: [PATCH] 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 --- modules/controlfreec/main.nf | 158 ++++++++++++++++++ modules/controlfreec/meta.yml | 183 +++++++++++++++++++++ tests/config/pytest_modules.yml | 4 + tests/config/test_data.config | 7 +- tests/modules/controlfreec/main.nf | 37 +++++ tests/modules/controlfreec/nextflow.config | 26 +++ tests/modules/controlfreec/test.yml | 22 +++ 7 files changed, 436 insertions(+), 1 deletion(-) create mode 100644 modules/controlfreec/main.nf create mode 100644 modules/controlfreec/meta.yml create mode 100644 tests/modules/controlfreec/main.nf create mode 100644 tests/modules/controlfreec/nextflow.config create mode 100644 tests/modules/controlfreec/test.yml diff --git a/modules/controlfreec/main.nf b/modules/controlfreec/main.nf new file mode 100644 index 00000000..21084f64 --- /dev/null +++ b/modules/controlfreec/main.nf @@ -0,0 +1,158 @@ +process CONTROLFREEC { + 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 + """ +} diff --git a/modules/controlfreec/meta.yml b/modules/controlfreec/meta.yml new file mode 100644 index 00000000..4d1e8674 --- /dev/null +++ b/modules/controlfreec/meta.yml @@ -0,0 +1,183 @@ +name: controlfreec +description: Copy number and genotype annotation from whole genome and whole exome sequencing data +keywords: + - cna + - cnv + - somatic + - single + - tumor-only +tools: + - controlfreec: + description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + homepage: http://boevalab.inf.ethz.ch/FREEC + documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html + tool_dev_url: https://github.com/BoevaLab/FREEC/ + doi: "10.1093/bioinformatics/btq635" + licence: ['GPL >=2'] + +input: + - args: + type: map + description: | + Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. + 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: + For default values, please check the documentation above. + + ``` + { + [ + "general" :[ + "bedgraphoutput": , + "breakpointthreshold": , + "breakpointtype": , + "coefficientofvariation": , + "contamination": , + "contaminationadjustment": , + "degree": , + "forcegccontentnormalization": , + "gccontentprofile": , + "intercept": , + "mincnalength": , + "minmappabilityperwindow": , + "minexpectedgc": , + "maxexpectedgc": , + "minimalsubclonepresence": , + "noisydata": , + "ploidy": , + "printNA": , + "readcountthreshold": , + "sex": , + "step": , + "telocentromeric": , + "uniquematch": , + "window": + ], + "control":[ + "inputformat": , + "mateorientation": , + ], + "sample":[ + "inputformat": , + "mateorientation": , + ], + "BAF":[ + "minimalcoverageperposition": , + "minimalqualityperposition": , + "shiftinquality": + ] + ] + } + ``` + + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mateFile_normal: + type: file + description: File with mapped reads + pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" + - mateFile_tumor: + type: file + description: File with mapped reads + pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" + - cpn_normal: + type: file + description: Raw copy number profiles (optional) + pattern: "*.cpn" + - cpn_tumor: + type: file + description: Raw copy number profiles (optional) + pattern: "*.cpn" + - minipileup_normal: + type: file + description: miniPileup file from previous run (optional) + pattern: "*.pileup" + - minipileup_tumor: + type: file + description: miniPileup file from previous run (optional) + pattern: "*.pileup" + - fasta: + type: file + description: Reference file (optional; required if args 'makePileup' is set) + pattern: "*.{fasta,fna,fa}" + - fai: + type: file + description: Fasta index + pattern: "*.fai" + - snp_position: + type: file + description: + pattern: "*.{}" + - known_snps: + type: file + description: File with known SNPs + pattern: "*.{vcf,vcf.gz}" + - known_snps_tbi: + type: file + description: Index of known_snps + pattern: "*.tbi" + - chr_directory: + type: file + description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided) + pattern: "*/" + - mappability: + type: file + description: Contains information of mappable positions (optional) + pattern: "*.gem" + - target_bed: + type: file + description: Sorted bed file containing capture regions (optional) + pattern: "*.bed" + + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - bedgraph: + type: file + 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" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index c553b9ce..f3cbaa33 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -356,6 +356,10 @@ cnvkit/batch: - modules/cnvkit/batch/** - tests/modules/cnvkit/batch/** +controlfreec: + - modules/controlfreec/** + - tests/modules/controlfreec/** + cooler/cload: - modules/cooler/cload/** - tests/modules/cooler/cload/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 7c3e183c..a3c26bcc 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -123,10 +123,12 @@ params { 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_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 = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" genome_21_multi_interval_bed_gz_tbi = "${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_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" @@ -156,7 +158,7 @@ params { justhusky_ped = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" justhusky_minimal_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" - + vcfanno_tar_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" } @@ -272,6 +274,9 @@ params { test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" test_genome21_indels_vcf_gz_tbi = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" diff --git a/tests/modules/controlfreec/main.nf b/tests/modules/controlfreec/main.nf new file mode 100644 index 00000000..576a845c --- /dev/null +++ b/tests/modules/controlfreec/main.nf @@ -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, + [] + ) +} diff --git a/tests/modules/controlfreec/nextflow.config b/tests/modules/controlfreec/nextflow.config new file mode 100644 index 00000000..5c4250be --- /dev/null +++ b/tests/modules/controlfreec/nextflow.config @@ -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" + ] + ] + } + } +} diff --git a/tests/modules/controlfreec/test.yml b/tests/modules/controlfreec/test.yml new file mode 100644 index 00000000..14c30205 --- /dev/null +++ b/tests/modules/controlfreec/test.yml @@ -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