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

nf-core/plasmidid @ 0.0.0-6c4ed3a

assembles bacterial plasmids

assembly plasmid bacterial

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @joseespinosa @drpatelh

Maintainers: @joseespinosa @drpatelh

assembles bacterial plasmids

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

include { PLASMIDID } from 'nf-core/plasmidid'

MIT License

Process

`Name`	`PLASMIDID`

Input 2 channels

#1 tuple

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

`fasta` file	FASTA reference file `*.{fasta,fa}`

Output 9 channels

#1 tab tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*final_results.tab` file	Results in a tabular file `*.{tab}`

#2 data tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/data/` directory	Directory containing the data produced by plasmidid `data`

#3 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*final_results.html` file	html file with results rendered `*.{html}`

#4 kmer tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/kmer/` directory	Directory containing the kmer files produced by plasmidid `database`

#5 logs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/logs/` directory	Directory containing the logs produced by plasmidid `logs`

#6 images tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/images/` directory	Directory containing the images produced by plasmidid `images`

#7 database tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/database/` directory	Directory containing the database produced by plasmidid `database`

#8 versions

`versions.yml` file	File containing software versions `versions.yml`

#9 fasta_files tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/fasta_files/` directory	Directory containing the fasta files produced by plasmidid `fasta_files`

Tool	Description	Homepage
plasmidid	Pipeline for plasmid identification and reconstruction	https://github.com/BU-ISCIII/plasmidID/wiki

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:37:32 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fplasmidid/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow