---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "chromograph"
description: Chromograph is a python package to create PNG images from genetics data such as BED and WIG files.
keywords:
  - chromosome_visualization
  - bed
  - wig
  - png
tools:
  - "chromograph":
      description: "Chromograph is a python package to create PNG images from genetics data such as BED and WIG files."
      homepage: "https://github.com/Clinical-Genomics/chromograph"
      documentation: "https://github.com/Clinical-Genomics/chromograph/blob/master/README.md"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta3:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta4:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta5:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta6:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta7:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - autozyg:
      type: file
      description: Bed file containing the regions of autozygosity
  - coverage:
      type: file
      description: Wig file containing the coverage information
  - exome:
      type: file
      description: Bed file containing the coverage for exome.
  - fracsnp:
      type: file
      description: Wig file containing the fraction of homozygous SNPs
  - ideogram:
      type: file
      description: |
        Bed file containing information necessary for ideogram plots.
        Format ['chrom', 'start', 'end', 'name', 'gStain']
  - regions:
      type: file
      description: Bed file containing UPD regions
  - sites:
      type: file
      description: Bed file containing UPD sites

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"
  - plots:
      type: file
      description: Directory containing the plots in png format
      pattern: "*.png"

authors:
  - "@ramprasadn"
