---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "vcf2cytosure"
description: Convert VCF with structural variations to CytoSure format
keywords:
  - structural_variants
  - array_cgh
  - vcf
  - cytosure
tools:
  - "vcf2cytosure":
      description: "Convert VCF with structural variations to CytoSure format"
      homepage: "https://github.com/NBISweden/vcf2cytosure"
      documentation: "https://github.com/NBISweden/vcf2cytosure"
      tool_dev_url: "https://github.com/NBISweden/vcf2cytosure"
      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 ]`
  - sv_vcf:
      type: file
      description: VCF file with structural variants
      pattern: "*.{vcf,vcf.gz}"
  - coverage_bed:
      type: file
      description: Bed file with coverage data
      pattern: "*.bed"
  - cns:
      type: file
      description: CN file from CNVkit, not compatible with coverage_bed file
  - snv_vcf:
      type: file
      description: |
        VCF file with SNVs to calculate probe coverage,
        not compatible with coverage_bed
        pattern: "*.{vcf,vcf.gz}"
  - blacklist_bed:
      type: file
      description: Bed file with regions to exclude
      pattern: "*.bed"

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"
  - cgh:
      type: file
      description: SV:s in CytoSure format
      pattern: "*.cgh"

authors:
  - "@jemten"
