name: picard_liftovervcf
description: Lifts over a VCF file from one reference build to another.
keywords:
  - vcf
  - picard
  - liftovervcf
tools:
  - picard:
      description: Move annotations from one assembly to another
      homepage: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
      tool_dev_url: https://github.com/broadinstitute/picard

      licence: ["MIT"]

input:
  - meta:
      type: map
      description: Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input_vcf:
      type: file
      description: VCF file
      pattern: "*.{vcf,vcf.gz}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: fasta file
      pattern: "*.fasta"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - dict:
      type: file
      description: dictionary for fasta file
      pattern: "*.{dict}"
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - chain:
      type: file
      description: The liftover chain file

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"
  - vcf_lifted:
      type: file
      description: VCF file containing successfully lifted variants
      pattern: "*.{lifted.vcf.gz}"
  - vcf_unlifted:
      type: file
      description: VCF file containing unsuccessfully lifted variants
      pattern: "*.{unlifted.vcf.gz}"

authors:
  - "@lucpen"
  - "@ramprasadn"
