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

versions.yml: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
funcscan
Github user louperelo
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