name: transdecoder_predict
description: TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf
keywords:
  - eukaryotes
  - gff

tools:
  - transdecoder:
      description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
      homepage: https://github.com/TransDecoder
      documentation: https://github.com/TransDecoder/TransDecoder/wiki
      tool_dev_url: https://github.com/TransDecoder/TransDecoder
      doi: ""
      licence: ['Broad Institute']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: fasta file
      pattern: "*.{fasta}"
  - fold:
      type: folder
      description: Output from the module transdecoder_longorf
      pattern: "*"

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"
  - pep:
      type: amino acids fasta file
      description: All ORFs meeting the minimum length criteria, regardless of coding potential
      pattern: "*.{pep}"
  - gff3:
      type: gff3 file
      description: Positions of all ORFs as found in the target transcripts
      pattern: "*.{gff3}"
  - cds:
      type: nucleotide fasta file
      description: the nucleotide coding sequence for all detected ORFs
      pattern: "*{cds}"
  - bed:
      type: bed file
      description: bed file
      pattern: "*{bed}"

authors:
  - "@Danilo2771"
