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

@@ -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
+    """
+}

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.
+      <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:
+      For default values, please check the documentation above.
+
+      ```
+      {
+        [
+          "general" :[
+              "bedgraphoutput": <optional>,
+              "breakpointthreshold": <optional>,
+              "breakpointtype": <optional>,
+              "coefficientofvariation": <optional>,
+              "contamination": <optional>,
+              "contaminationadjustment": <optional>,
+              "degree": <optional>,
+              "forcegccontentnormalization": <optional>,
+              "gccontentprofile": <optional>,
+              "intercept": <optional>,
+              "mincnalength": <optional>,
+              "minmappabilityperwindow": <optional>,
+              "minexpectedgc": <optional>,
+              "maxexpectedgc": <optional>,
+              "minimalsubclonepresence": <optional>,
+              "noisydata": <optional>,
+              "ploidy": <optional>,
+              "printNA": <optional>,
+              "readcountthreshold": <optional >,
+              "sex": <optional>,
+              "step": <optional value>,
+              "telocentromeric": <optional>,
+              "uniquematch": <optional>,
+              "window": <optional>
+          ],
+          "control":[
+              "inputformat": <required>,
+              "mateorientation": <optional>,
+          ],
+          "sample":[
+              "inputformat": <required>,
+              "mateorientation": <optional>,
+          ],
+          "BAF":[
+              "minimalcoverageperposition": <optional>,
+              "minimalqualityperposition": <optional>,
+              "shiftinquality": <optional>
+          ]
+        ]
+      }
+      ```
+
+  - 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"

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/**

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"
 

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,
+                            []
+                        )
+}

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"
+                    ]
+                    ]
+        }
+    }
+}

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