Nextflow Registry | nf-core/prokka@0.0.0-6c4ed3a

nf-core/prokka @ 0.0.0-6c4ed3a

Whole genome annotation of small genomes (bacterial, archeal, viral)

annotation fasta prokka

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @rpetit3

Maintainers: @rpetit3

Whole genome annotation of small genomes (bacterial, archeal, viral)

Add the following snippet to your workflow script to include this module.

include { PROKKA } from 'nf-core/prokka'

MIT License

Process

`Name`	`PROKKA`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA file to be annotated. Has to contain at least a non-empty string dummy value.

`proteins` file	FASTA file of trusted proteins to first annotate from (optional)

`prodigal_tf` file	Training file to use for Prodigal (optional)

Output 13 channels

#1 err tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.err` file	unacceptable annotations - the NCBI discrepancy report. `*.{err}`

#2 faa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.faa` file	protein FASTA file of the translated CDS sequences `*.{faa}`

#3 ffn tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.ffn` file	nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) `*.{ffn}`

#4 fna tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.fna` file	nucleotide FASTA file of the input contig sequences `*.{fna}`

#5 fsa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.fsa` file	nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file `*.{fsa}`

#6 gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.gbk` file	annotation in GenBank format, containing both sequences and annotations `*.{gbk}`

#7 gff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.gff` file	annotation in GFF3 format, containing both sequences and annotations `*.{gff}`

#8 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.log` file	contains all the output that Prokka produced during its run `*.{log}`

#9 sqn tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.sqn` file	an ASN1 format "Sequin" file for submission to Genbank `*.{sqn}`

#10 tbl tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.tbl` file	feature Table file, used by "tbl2asn" to create the .sqn file `*.{tbl}`

#11 tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]