Nextflow Registry | nf-core/ensemblvep/vep@0.0.0-6c4ed3a

nf-core/ensemblvep/vep @ 0.0.0-6c4ed3a

Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through task.ext.args.

annotation vcf json tab

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @maxulysse @matthdsm @nvnieuwk

Maintainers: @maxulysse @matthdsm @nvnieuwk

Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through task.ext.args.

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

include { ENSEMBLVEP_VEP } from 'nf-core/ensemblvep/vep'

MIT License

Process

`Name`	`ENSEMBLVEP_VEP`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	vcf to annotate
`custom_extra_files` file	extra sample-specific files to be used with the `--custom` flag to be configured with ext.args (optional)

`genome` string	which genome to annotate with

`species` string	which species to annotate with

`cache_version` integer	which version of the cache to annotate with

#5 tuple

`meta2` map	Groovy Map containing cache information e.g. [ id:'test' ]
`cache` file	path to VEP cache (optional)

#6 tuple

`meta3` map	Groovy Map containing fasta reference information e.g. [ id:'test' ]
`fasta` file	reference FASTA file (optional) `*.{fasta,fa}`

`extra_files` file	path to file(s) needed for plugins (optional)

Output 8 channels

#1 tab tuple

`meta` map	Map with sample information
`${prefix}.tab.gz` file	tab file with annotated variants (optional) `*.ann.tab.gz`

#2 tbi tuple

`meta` map	Map with sample information
`${prefix}.vcf.gz.tbi` file	annotated vcf index (optional) `*.vcf.gz.tbi`

#3 vcf tuple

`meta` map	Map with sample information
`${prefix}.vcf.gz` file	annotated vcf (optional) `*.vcf.gz`

#4 json tuple

`meta` map	Map with sample information
`${prefix}.json.gz` file	json file with annotated variants (optional) `*.ann.json.gz`

#5 report tuple

#6 versions_tabix tuple

`${task.process}` string	The process
`tabix` string	The tool name
`tabix -h 2>&1 \| grep -oP 'Version:\s*\K[^\s]+'` eval	The expression to obtain the version of the tool

#7 versions_ensemblvep tuple