nf-core_modules/modules/bakta/meta.yml

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name: bakta
description: Rapid annotation of bacterial genomes & plasmids.
keywords:
- annotation
- fasta
- prokaryote
tools:
- bakta:
description: Rapid & standardized annotation of bacterial genomes & plasmids.
homepage: https://github.com/oschwengers/bakta
documentation: https://github.com/oschwengers/bakta
tool_dev_url: https://github.com/oschwengers/bakta
doi: "10.1099/mgen.0.000685"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: |
FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
- db:
type: file
description: |
Path to the Bakta database
- proteins:
type: file
description: FASTA file of trusted proteins to first annotate from (optional)
- prodigal_tf:
type: file
description: Training file to use for Prodigal (optional)
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- tsv:
type: file
description: annotations as simple human readble tab separated values
pattern: "*.tsv"
- gff:
type: file
description: annotations & sequences in GFF3 format
pattern: "*.gff3"
- gbff:
type: file
description: annotations & sequences in (multi) GenBank format
pattern: "*.gbff"
- embl:
type: file
description: annotations & sequences in (multi) EMBL format
pattern: "*.embl"
- fna:
type: file
description: replicon/contig DNA sequences as FASTA
pattern: "*.fna"
- faa:
type: file
description: CDS/sORF amino acid sequences as FASTA
pattern: "*.faa"
- ffn:
type: file
description: feature nucleotide sequences as FASTA
pattern: "*.ffn"
- hypotheticals_tsv:
type: file
description: further information on hypothetical protein CDS as simple human readble tab separated values
pattern: "*.hypotheticals.tsv"
- hypotheticals_faa:
type: file
description: hypothetical protein CDS amino acid sequences as FASTA
pattern: "*.hypotheticals.faa"
authors:
- "@rpetit3"