name: ascat
description: copy number profiles of tumour cells.
keywords:
  - sort
tools:
  - ascat:
      description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).
      homepage: None
      documentation: None
      tool_dev_url: https://github.com/Crick-CancerGenomics/ascat
      doi: "10.1093/bioinformatics/btaa538"
      licence: ['GPL v3']

input:
  - args:
      type: map
      description: |
        Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. <optional> parameters can be removed from the map, if they are not set. For default values, please check the documentation above.

        ```
        {
          [
            "gender": "XX",
            "genomeVersion": "hg19"
            "purity": <optional>,
            "ploidy": <optional>,
            "gc_files": <optional>,
            "minCounts": <optional>,
            "chrom_names": <optional>,
            "min_base_qual": <optional>,
            "min_map_qual": <optional>,
            "ref_fasta": <optional>,
            "skip_allele_counting_tumour": <optional>,
            "skip_allele_counting_normal": <optional>
          ]
        }
        ```

  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input_normal:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - index_normal:
      type: file
      description: index for normal_bam
      pattern: "*.{bai}"
  - input_tumor:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - index_tumor:
      type: file
      description: index for tumor_bam
      pattern: "*.{bai}"
  - allele_files:
      type: file
      description: allele files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
  - loci_files:
      type: file
      description: loci files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
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"
  - png:
      type: file
      description: ASCAT plots
      pattern: "*.{png}"
  - purityploidy:
      type: file
      description: purity and ploidy data
      pattern: "*.purityploidy.txt"
  - segments:
      type: file
      description: segments data
      pattern: "*.segments.txt"
authors:
  - "@aasNGC"
  - "@lassefolkersen"
  - "@FriederikeHanssen"
  - "@maxulysse"