---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "metaeuk_easypredict"
description: Annotation of eukaryotic metagenomes using MetaEuk
keywords:
  - genomics
  - annotation
  - fasta
tools:
  - "metaeuk":
      description: "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics"
      homepage: https://github.com/soedinglab/metaeuk
      documentation: https://github.com/soedinglab/metaeuk
      tool_dev_url: https://github.com/soedinglab/metaeuk
      doi: "10.1186/s40168-020-00808-x"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - fasta:
      type: file
      description: Nucleotide FASTA file for annotation
      pattern: "*.{fasta,fa,fasta.gz,fa.gz}"

  - database:
      type: file
      description: Either a fasta file containing protein sequences, or a directory containing an mmseqs2-formatted protein database

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"

  - faa:
      type: file
      description: Protein FASTA file containing the exons from the input FASTA file
      pattern: "*.{fas}"

  - codon:
      type: file
      description: Nucleotide FASTA file of protein-coding sequences
      pattern: "*.{codon.fas}"

  - tsv:
      type: file
      description: TSV file containing locations of each protein coding sequence in the input fasta
      pattern: "*.headersMap.{tsv}"

  - gff:
      type: file
      description: Annotation file in GFF format
      pattern: "*.{gff}"

authors:
  - "@prototaxites"
