nf-core_modules/modules/transdecoder/predict/meta.yml

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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"