Nextflow Registry | nf-core/checkv/endtoend@0.0.0-6c4ed3a

nf-core/checkv/endtoend @ 0.0.0-6c4ed3a

Assess the quality of metagenome-assembled viral genomes.

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @Joon-Klaps

Maintainers: @Joon-Klaps

Assess the quality of metagenome-assembled viral genomes.

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

include { CHECKV_ENDTOEND } from 'nf-core/checkv/endtoend'

MIT License

Process

`Name`	`CHECKV_ENDTOEND`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	fasta file `*.{fasta,fna,fa}`

`db` directory	Directory pointing to checkV database

Output 7 channels

#1 viruses tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ]
`${prefix}/viruses.fna` file	CheckV's extracted virus contigs `${prefix}/viruses.fna`

#2 proviruses tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ]
`${prefix}/proviruses.fna` file	CheckV's extracted proviruses contigs `${prefix}/proviruses.fna`

#3 completeness tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ]
`${prefix}/completeness.tsv` file	CheckV's detailed overview table on estimating completeness `${prefix}/completeness.tsv`

#4 contamination tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ]
`${prefix}/contamination.tsv` file	CheckV's detailed overview table on estimating contamination `${prefix}/contamination.tsv`

#5 quality_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ]
`${prefix}/quality_summary.tsv` file	CheckV's main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs `${prefix}/quality_summary.tsv`

#6 versions_checkv tuple

`${task.process}` string	The name of the process
`checkv` string	The name of the tool
`checkv -h 2>&1 \| sed '1!d;s/^.CheckV v//;s/:.//'` eval	The expression to obtain the version of the tool

#7 complete_genomes tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ]
`${prefix}/complete_genomes.tsv` file	CheckV's detailed overview table on the identified putative complete genomes `${prefix}/complete_genomes.tsv`

Tool	Description	Homepage
checkv	Assess the quality of metagenome-assembled viral genomes.	https://bitbucket.org/berkeleylab/checkv/src/master/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:09:03 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcheckv%2Fendtoend/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/checkv/endtoend/blobs/sha256:c618bb140e0917fa2792fb6c26500c2858ccb0519757a8d188bcbff3b6d0579f
Size	3.0 KB