vcf_annotate_ensemblvep_snpeff

Perform annotation with ensemblvep and/or snpeff and bgzip + tabix index the resulting VCF file. This subworkflow uses the scatter-gather method to run VEP/snpEff in parallel to increase throughput. The input VCF is split into multiple smaller VCFs of fixed size, which are annotated separately and concatenated back together to a single output file per sample. Only VCF/BCF outputs are currently supported.

vcfannotationensemblvepsnpeff

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

Description

Input

name:type

description

pattern

`ch_vcf`

vcf file to annotate
Structure: [ val(meta), path(vcf), path(tbi) ]

`ch_fasta`

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

`val_vep_genome :string`

genome to use for ensemblvep

`val_vep_species :string`

species to use for ensemblvep

`val_vep_cache_version :integer`

cache version to use for ensemblvep

`ch_vep_cache`

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

`ch_vep_extra_files`

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

`val_snpeff_db :string`

database to use for snpeff, usually consists of the genome and the database version
e.g. WBcel235.105

`ch_snpeff_cache`

the root cache folder for snpeff (optional)
Structure: [ path(cache) ]

`val_tools_to_use :list`

The tools to use. Options => ’[“ensemblvep”, “snpeff”]’

`val_sites_per_chunk :integer`

The amount of variants per scattered VCF.
Set this value to null, [] or false to disable scattering.

Output

name:type

description

pattern

`vcf_tbi`

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

`vep_reports :file`

html reports generated by Ensembl VEP

*.html

`snpeff_reports`

csv reports generated by snpeff
Structure: [ val(meta), path(csv) ]

`snpeff_html`

html reports generated by snpeff
Structure: [ val(meta), path(html) ]

`snpeff_genes`

txt (tab separated) file having counts of the number of variants
affecting each transcript and gene
Structure: [ val(meta), path(txt) ]

`versions :file`

File containing software versions

versions.yml