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).
      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"]
      identifier: biotools:ascat
input:
  - - 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:
  - allelefreqs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*alleleFrequencies_chr*.txt":
          type: file
          description: Files containing allee frequencies per chromosome
          pattern: "*{alleleFrequencies_chr*.txt}"
  - bafs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*BAF.txt":
          type: file
          description: BAF file
  - cnvs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*cnvs.txt":
          type: file
          description: CNV file
  - logrs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*LogR.txt":
          type: file
          description: LogR file
  - metrics:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*metrics.txt":
          type: file
          description: File containing quality metrics
          pattern: "*.{metrics.txt}"
  - png:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*png":
          type: file
          description: ASCAT plots
          pattern: "*.{png}"
  - purityploidy:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*purityploidy.txt":
          type: file
          description: File with purity and ploidy data
          pattern: "*.{purityploidy.txt}"
  - segments:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*segments.txt":
          type: file
          description: File with segments data
          pattern: "*.{segments.txt}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@aasNGC"
  - "@lassefolkersen"
  - "@FriederikeHanssen"
  - "@maxulysse"
  - "@SusiJo"
maintainers:
  - "@aasNGC"
  - "@lassefolkersen"
  - "@FriederikeHanssen"
  - "@maxulysse"
  - "@SusiJo"
