name: ichorcna_createpon
description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals
keywords:
  - ichorcna
  - cnv
  - cna
  - cfDNA
  - wgs
  - panel_of_normals
tools:
  - ichorcna:
      description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
      homepage: https://github.com/broadinstitute/ichorCNA
      documentation: https://github.com/broadinstitute/ichorCNA/wiki
      tool_dev_url: https://github.com/broadinstitute/ichorCNA
      doi: "10.1038/s41467-017-00965-y"
      licence: ["GPL v3"]

input:
  - wigs:
      type: file
      description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals.
      pattern: "*.{wig}"

  - gc_wig:
      type: file
      description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
      pattern: "*.{wig}"

  - map_wig:
      type: file
      description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
      pattern: "*.{wig}"

  - centromere:
      type: file
      description: Text file giving centromere locations of each genome, to exclude these windows
      pattern: "*.{txt}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

  - rds:
      type: file
      description: R data file (.rds) containing panel of normals data, medians of each bin.
      pattern: "*.rds"

  - txt:
      type: file
      description: Text file containing panel of normals data, medians of each bin.
      pattern: "*.txt"

authors:
  - "@sppearce"