snpeff/snpeff_download

annotation

database

download

snp

variant

snpeff

Description

Download a pre-built SnpEff reference genome/annotation database.

Type

bash_script

License

MIT

Keywords

annotation

database

download

snp

variant

snpeff

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.data_dir"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/snpeff/snpeff_download/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--genome_version	string required	Reference genome/database version to download.

Name

Type & Properties

--genome_version

string

required

Outputs

Name	Type & Properties	Description
--output	file required output	Directory in which the downloaded database is stored

Name

Type & Properties

--output

file

required

output

Generic options

Name	Type & Properties	Description
--config -c	file	Specify config file.
--config_option	string	Override a config file option (name=value).
--debug -d	boolean_true	Debug mode (very verbose).
--no_log	boolean_true	Do not report usage statistics to server.
--quiet -q	boolean_true	Quiet mode (do not show any messages or errors).
--verbose -v	boolean_true	Verbose mode.

Name

Type & Properties

--config

-c

file

--config_option

string

--debug

-d

boolean_true

--no_log

boolean_true

--quiet

-q

boolean_true

--verbose

-v

boolean_true