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{:bash}

:map

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

fasta{:bash}

:file

FASTA file

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

output_format{:bash}

:string

Output format

{gbk,gff}

Output

name:type
description
pattern

annotations{:bash}

meta{:bash}

:map

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

*.${output_format}.gz{:bash}

:file

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

*.{gbk,gff}.gz

fna{:bash}

meta{:bash}

:map

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

*.fna.gz{:bash}

:file

nucleotide sequences file

*.{fna.gz}

faa{:bash}

meta{:bash}

:map

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

*.faa.gz{:bash}

:file

protein translations file

*.{faa.gz}

score{:bash}

meta{:bash}

:map

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

*.score.gz{:bash}

:file

all potential genes (with scores)

*.{score.gz}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
funcscan
maintainer
Github user louperelo
get in touch
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