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"