vcf_annotate_ensemblvep

Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file

vcfannotationensemblvep

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

Description

Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file

Input

name

description

pattern

`ch_vcf`

vcf file to annotate
Structure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)… (optional)] ]

`ch_fasta`

Reference genome fasta file (optional)
Structure: [ val(meta2), path(fasta) ]

`val_genome`

genome to use

`val_species`

species to use

`val_cache_version`

cache version to use

`ch_cache`

the root cache folder for ensemblvep (optional)
Structure: [ val(meta3), path(cache) ]

`ch_extra_files`

any extra files needed by plugins for ensemblvep (optional)
Structure: [ path(file1), path(file2)… ]

`ch_gtf`

sorted, bgzipped GTF file (+ tabix index) to annotate with instead of a cache (optional).
Mutually exclusive with ch_cache.
Structure: [ path(gtf), path(gtf_tbi) ]

Output

name

description

pattern

`vcf_tbi`

Compressed vcf file + tabix index
Structure: [ val(meta), path(vcf), path(tbi) ]

`json`

json file
Structure: [ val(meta), path(json) ]

`tab`

tab file
Structure: [ val(meta), path(tab) ]

`reports`

html reports

*.html

`versions`

File containing software versions

versions.yml