nf-core_modules/modules/prokka/meta.yml

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name: prokka
description: Whole genome annotation of small genomes (bacterial, archeal, viral)
keywords:
- annotation
- fasta
- prokka
tools:
- prokka:
description: Rapid annotation of prokaryotic genomes
homepage: https://github.com/tseemann/prokka
doi: "10.1093/bioinformatics/btu153"
licence: ['GPL v2']
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.
- 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 ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- gff:
type: file
description: annotation in GFF3 format, containing both sequences and annotations
pattern: "*.{gff}"
- gbk:
type: file
description: annotation in GenBank format, containing both sequences and annotations
pattern: "*.{gbk}"
- fna:
type: file
description: nucleotide FASTA file of the input contig sequences
pattern: "*.{fna}"
- faa:
type: file
description: protein FASTA file of the translated CDS sequences
pattern: "*.{faa}"
- ffn:
type: file
description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)
pattern: "*.{ffn}"
- sqn:
type: file
description: an ASN1 format "Sequin" file for submission to Genbank
pattern: "*.{sqn}"
- fsa:
type: file
description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file
pattern: "*.{fsa}"
- tbl:
type: file
description: feature Table file, used by "tbl2asn" to create the .sqn file
pattern: "*.{tbl}"
- err:
type: file
description: unacceptable annotations - the NCBI discrepancy report.
pattern: "*.{err}"
- log:
type: file
description: contains all the output that Prokka produced during its run
pattern: "*.{log}"
- txt:
type: file
description: statistics relating to the annotated features found
pattern: "*.{txt}"
- tsv:
type: file
description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)
pattern: "*.{tsv}"
authors:
- "@rpetit3"