modules/pyrodigal

Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.

sortannotationpredictionprokaryote

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

Description

Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

FASTA file

*.{fasta.gz,fa.gz,fna.gz}

`output_format`
`:string`

Output format

{gbk,gff}

Output

name:type

description

pattern

`annotations`

`meta`
`:map`

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

`*.${output_format}.gz`
`:file`

Gene annotations. The file format is specified via input channel “output_format”.

*.{gbk,gff}.gz

`fna`

`meta`
`:map`

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

`*.fna.gz`
`:file`

nucleotide sequences file

*.{fna.gz}

`faa`

`meta`
`:map`

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

`*.faa.gz`
`:file`

protein translations file

*.{faa.gz}

`score`

`meta`
`:map`

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

`*.score.gz`
`:file`

all potential genes (with scores)

*.{score.gz}

`versions_pyrodigal`

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

The name of the process

`pyrodigal`
`:string`

The name of the tool

`pyrodigal --version |& sed 's/pyrodigal v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`pyrodigal`
`:string`

The name of the tool

`pyrodigal --version |& sed 's/pyrodigal v//'`
`:eval`

The expression to obtain the version of the tool

Tools

pyrodigal
GPL v3

Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython.

pyrodigal.readthedocs.org https://github.com/althonos/pyrodigal/ 10.21105/joss.04296

modules/pyrodigal

Description

Input

`meta`
`:map`

`fasta`
`:file`

`output_format`
`:string`

Output

`annotations`

`meta`
`:map`

`*.${output_format}.gz`
`:file`

`fna`

`meta`
`:map`

`*.fna.gz`
`:file`

`faa`

`meta`
`:map`

`*.faa.gz`
`:file`

`score`

`meta`
`:map`

`*.score.gz`
`:file`

`versions_pyrodigal`

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

`pyrodigal`
`:string`

`pyrodigal --version |& sed 's/pyrodigal v//'`
`:eval`

Topics

`versions`

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

`pyrodigal`
`:string`

`pyrodigal --version |& sed 's/pyrodigal v//'`
`:eval`

Tools

pyrodigal
GPL v3

included in

maintainer

get in touch

modules/pyrodigal

Description

Input

meta:map

fasta:file

output_format:string

Output

annotations

meta:map

*.${output_format}.gz:file

fna

meta:map

*.fna.gz:file

faa

meta:map

*.faa.gz:file

score

meta:map

*.score.gz:file

versions_pyrodigal

${task.process}:string

pyrodigal:string

pyrodigal --version |& sed 's/pyrodigal v//':eval

Topics

versions

${task.process}:string

pyrodigal:string

pyrodigal --version |& sed 's/pyrodigal v//':eval

Tools

pyrodigal GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`output_format`
`:string`

`annotations`

`meta`
`:map`

`*.${output_format}.gz`
`:file`

`fna`

`meta`
`:map`

`*.fna.gz`
`:file`

`faa`

`meta`
`:map`

`*.faa.gz`
`:file`

`score`

`meta`
`:map`

`*.score.gz`
`:file`

`versions_pyrodigal`

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

`pyrodigal`
`:string`

`pyrodigal --version |& sed 's/pyrodigal v//'`
`:eval`

`versions`

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

`pyrodigal`
`:string`

`pyrodigal --version |& sed 's/pyrodigal v//'`
`:eval`

pyrodigal
GPL v3