# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "liftoff"
description: |
  Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same,
  or closely-related species
keywords:
  - genome
  - annotation
  - gff3
  - gtf
  - liftover
tools:
  - "liftoff":
      description: |
        Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same,
        or closely-related species
      homepage: "https://github.com/agshumate/Liftoff"
      documentation: "https://github.com/agshumate/Liftoff"
      tool_dev_url: "https://github.com/agshumate/Liftoff"
      doi: "10.1093/bioinformatics/bty191"
      licence: ["GPL v3 License"]
      identifier: biotools:liftoff
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'test' ]`
    - target_fa:
        type: file
        description: Target assembly in fasta format (can be gzipped)
        pattern: "*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}"
  - - ref_fa:
        type: file
        description: Reference assembly in fasta format (can be gzipped)
        pattern: "*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}"
  - - ref_annotation:
        type: file
        description: Reference assembly annotations in gtf or gff3 format
        pattern: "*.{gtf,gff3}"
  - - ref_db:
        type: file
        description: |
          Name of feature database; if not specified, the -g argument must
          be provided and a database will be built automatically
output:
  - gff3:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'test' ]`
      - ${prefix}.gff3:
          type: file
          description: Lifted annotations for the target assembly in gff3 format
          pattern: "*.gff3"
  - polished_gff3:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'test' ]`
      - "*.polished.gff3":
          type: file
          description: Polished lifted annotations for the target assembly in gff3 format
          pattern: "*.polished.gff3"
  - unmapped_txt:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'test' ]`
      - "*.unmapped.txt":
          type: file
          description: List of unmapped reference annotations
          pattern: "*.unmapped.txt"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@GallVp"
maintainers:
  - "@GallVp"
