nf-core_modules/modules/controlfreec/meta.yml

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"