utils_annotation_cache

Check the path to the annotation cache depending if local or on the cloud, or using annotation-cache itself

snpeffensemblvepannotation-cacheannotationcacheverification

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/utils_annotation_cache

Description

Check the path to the annotation cache depending if local or on the cloud, or using annotation-cache itself

Input

name

description

pattern

`ensemblvep_cache`

Path to root cache
Structure: [ path(cache) ]

`ensemblvep_cache_version`

cache_version to use
Structure: [ val(cache_version) ]

`ensemblvep_custom_args`

custom args, to check if refseq or merged is needed
Structure: [ val(custom args) ]

`ensemblvep_genome`

genome to use
Structure: [ val(genome) ]

`ensemblvep_species`

species to use
Structure: [ val(species) ]

`ensemblvep_enabled`

Boolean to enable ensemblvep
Structure: [ Boolean ]

`snpeff_cache`

Path to root cache
Structure: [ path(cache) ]

`snpeff_db`

db to use
Structure: [ val(db) ]

`snpeff_enabled`

Boolean to enable snpeff
Structure: [ Boolean ]

`help_message`

Extra help message to display when error
Structure: [ val(species) ]

Output

name

description

pattern

`ensemblvep_cache`

Path to ensemblvep cache
Structure: [ val(meta), path(cache) ]

`snpeff_cache`

Path to snpeff cache
Structure: [ val(meta), path(cache) ]

utils_annotation_cache

Description

Input

`ensemblvep_cache`

`ensemblvep_cache_version`

`ensemblvep_custom_args`

`ensemblvep_genome`

`ensemblvep_species`

`ensemblvep_enabled`

`snpeff_cache`

`snpeff_db`

`snpeff_enabled`

`help_message`

Output

`ensemblvep_cache`

`snpeff_cache`

included modules and subworkflows

maintainer

get in touch