name: ascat
description: copy number profiles of tumour cells.
keywords:
  - bam
  - copy number
  - cram
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: https://github.com/VanLoo-lab/ascat/tree/master/man
      tool_dev_url: https://github.com/VanLoo-lab/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),
            "BED_file": (optional) but recommended for WES,
            "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 file, must adhere to chr1, chr2, ...chrX notation
        For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.
      pattern: "*.{bam,cram}"
  - index_normal:
      type: file
      description: index for normal_bam/cram
      pattern: "*.{bai,crai}"
  - input_tumor:
      type: file
      description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation
      pattern: "*.{bam,cram}"
  - index_tumor:
      type: file
      description: index for tumor_bam/cram
      pattern: "*.{bai,crai}"
  - allele_files:
      type: file
      description: allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
  - loci_files:
      type: file
      description:
        loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
        Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command
        `if [[ $(samtools view <your_bam_file.bam> | head -n1 | cut -f3)\" == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`
  - bed_file:
      type: file
      description: Bed file for ASCAT WES (optional, but recommended for WES)
  - fasta:
      type: file
      description: Reference fasta file (optional)
  - gc_file:
      type: file
      description: GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content
  - rt_file:
      type: file
      description: replication timing correction file (optional, provide only in combination with gc_file)
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - allelefreqs:
      type: file
      description: Files containing allee frequencies per chromosome
      pattern: "*{alleleFrequencies_chr*.txt}"
  - metrics:
      type: file
      description: File containing quality metrics
      pattern: "*.{metrics.txt}"
  - png:
      type: file
      description: ASCAT plots
      pattern: "*.{png}"
  - purityploidy:
      type: file
      description: File with purity and ploidy data
      pattern: "*.{purityploidy.txt}"
  - segments:
      type: file
      description: File with segments data
      pattern: "*.{segments.txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@aasNGC"
  - "@lassefolkersen"
  - "@FriederikeHanssen"
  - "@maxulysse"
  - "@SusiJo"