modules/transdecoder_predict

TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf

eukaryotesgffcdstranscroder

https://github.com/nf-core/modules/[...]/modules/nf-core/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

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

fasta file

*.{fasta}

`fold`
`:directory`

Output from the module transdecoder_longorf

*

Output

name:type

description

pattern

`pep`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.transdecoder.pep`
`:file`

All ORFs meeting the minimum length criteria, regardless of coding potential

*.{pep}

`gff3`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.transdecoder.gff3`
`:file`

Positions of all ORFs as found in the target transcripts

*.{gff3}

`cds`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.transdecoder.cds`
`:file`

the nucleotide coding sequence for all detected ORFs

*{cds}

`bed`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.transdecoder.bed`
`:file`

bed file

*{bed}

`versions_transdecoder`

`${task.process}`
`:string`

The name of the process

`transdecoder`
`:string`

The name of the tool

`TransDecoder.Predict --version | sed 's/TransDecoder.Predict //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`transdecoder`
`:string`

The name of the tool

`TransDecoder.Predict --version | sed 's/TransDecoder.Predict //'`
`:eval`

The expression to obtain the version of the tool

Tools

transdecoder
Broad Institute

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.

github.com/TransDecoder github.com/TransDecoder/TransDecoder/wiki https://github.com/TransDecoder/TransDecoder

modules/transdecoder_predict

Description

Input

`meta`
`:map`

`fasta`
`:file`

`fold`
`:directory`

Output

`pep`

`meta`
`:map`

`*.transdecoder.pep`
`:file`

`gff3`

`meta`
`:map`

`*.transdecoder.gff3`
`:file`

`cds`

`meta`
`:map`

`*.transdecoder.cds`
`:file`

`bed`

`meta`
`:map`

`*.transdecoder.bed`
`:file`

`versions_transdecoder`

`${task.process}`
`:string`

`transdecoder`
`:string`

`TransDecoder.Predict --version | sed 's/TransDecoder.Predict //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`transdecoder`
`:string`

`TransDecoder.Predict --version | sed 's/TransDecoder.Predict //'`
`:eval`

Tools

transdecoder
Broad Institute

maintainer

get in touch

modules/transdecoder_predict

Description

Input

meta :map

fasta :file

fold :directory

Output

pep

meta :map

*.transdecoder.pep :file

gff3

meta :map

*.transdecoder.gff3 :file

cds

meta :map

*.transdecoder.cds :file

bed

meta :map

*.transdecoder.bed :file

versions_transdecoder

${task.process} :string

transdecoder :string

TransDecoder.Predict --version | sed 's/TransDecoder.Predict //' :eval

Topics

versions

${task.process} :string

transdecoder :string

TransDecoder.Predict --version | sed 's/TransDecoder.Predict //' :eval

Tools

transdecoderBroad Institute

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`fold`
`:directory`

`pep`

`meta`
`:map`

`*.transdecoder.pep`
`:file`

`gff3`

`meta`
`:map`

`*.transdecoder.gff3`
`:file`

`cds`

`meta`
`:map`

`*.transdecoder.cds`
`:file`

`bed`

`meta`
`:map`

`*.transdecoder.bed`
`:file`

`versions_transdecoder`

`${task.process}`
`:string`

`transdecoder`
`:string`

`TransDecoder.Predict --version | sed 's/TransDecoder.Predict //'`
`:eval`

`versions`

`${task.process}`
`:string`

`transdecoder`
`:string`

`TransDecoder.Predict --version | sed 's/TransDecoder.Predict //'`
`:eval`

transdecoder
Broad Institute