subworkflows/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

`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) ]

`reports` (file)

html reports

*.html

`versions` (file)

File containing software versions

versions.yml

subworkflows/vcf_annotate_ensemblvep_snpeff

Description

Input

`ch_vcf`

`ch_fasta`

`val_vep_genome` (string)

`val_vep_species` (string)

`val_vep_cache_version` (integer)

`ch_vep_cache`

`ch_vep_extra_files`

`val_snpeff_db` (string)

`ch_snpeff_cache`

`val_tools_to_use` (list)

`val_sites_per_chunk` (integer)

Output

`vcf_tbi`

`reports` (file)

`versions` (file)

included modules and subworkflows

maintainers

get in touch

subworkflows/vcf_annotate_ensemblvep_snpeff

Description

Input

ch_vcf

ch_fasta

val_vep_genome (string)

val_vep_species (string)

val_vep_cache_version (integer)

ch_vep_cache

ch_vep_extra_files

val_snpeff_db (string)

ch_snpeff_cache

val_tools_to_use (list)

val_sites_per_chunk (integer)

Output

vcf_tbi

reports (file)

versions (file)

included modules and subworkflows

maintainers

get in touch

`ch_vcf`

`ch_fasta`

`val_vep_genome` (string)

`val_vep_species` (string)

`val_vep_cache_version` (integer)

`ch_vep_cache`

`ch_vep_extra_files`

`val_snpeff_db` (string)

`ch_snpeff_cache`

`val_tools_to_use` (list)

`val_sites_per_chunk` (integer)

`vcf_tbi`

`reports` (file)

`versions` (file)