modules/prodigal

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

prokaryotesgene findingmicrobial

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

Description

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

Input

name:type

description

pattern

`meta`
`:map`

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

`genome`
`:file`

fasta/fasta.gz file

`output_format`
`:string`

Output format (“gbk”/“gff”/“sqn”/“sco”)

Output

name:type

description

pattern

`gene_annotations`

`meta`
`:map`

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

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

gene annotations in output_format given as input

*.{output_format}

`nucleotide_fasta`

`meta`
`:map`

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

`${prefix}.fna.gz`
`:file`

nucleotide sequences file

*.{fna}

`amino_acid_fasta`

`meta`
`:map`

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

`${prefix}.faa.gz`
`:file`

protein translations file

*.{faa}

`all_gene_annotations`

`meta`
`:map`

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

`${prefix}_all.txt.gz`
`:file`

complete starts file

*.{_all.txt}

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

prodigal
GPL v3

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

github.com/hyattpd/Prodigal github.com/hyattpd/prodigal/wiki https://github.com/hyattpd/Prodigal 10.1186/1471-2105-11-119

modules/prodigal

Description

Input

`meta`
`:map`

`genome`
`:file`

`output_format`
`:string`

Output

`gene_annotations`

`meta`
`:map`

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

`nucleotide_fasta`

`meta`
`:map`

`${prefix}.fna.gz`
`:file`

`amino_acid_fasta`

`meta`
`:map`

`${prefix}.faa.gz`
`:file`

`all_gene_annotations`

`meta`
`:map`

`${prefix}_all.txt.gz`
`:file`

`versions`

`versions.yml`
`:file`

Tools

prodigal
GPL v3

included in

maintainer

get in touch

modules/prodigal

Description

Input

meta:map

genome:file

output_format:string

Output

gene_annotations

meta:map

${prefix}.${output_format}.gz:file

nucleotide_fasta

meta:map

${prefix}.fna.gz:file

amino_acid_fasta

meta:map

${prefix}.faa.gz:file

all_gene_annotations

meta:map

${prefix}_all.txt.gz:file

versions

versions.yml:file

Tools

prodigal GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`genome`
`:file`

`output_format`
`:string`

`gene_annotations`

`meta`
`:map`

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

`nucleotide_fasta`

`meta`
`:map`

`${prefix}.fna.gz`
`:file`

`amino_acid_fasta`

`meta`
`:map`

`${prefix}.faa.gz`
`:file`

`all_gene_annotations`

`meta`
`:map`

`${prefix}_all.txt.gz`
`:file`

`versions`

`versions.yml`
`:file`

prodigal
GPL v3