Description

Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)

Input

name:type
description
pattern

dataset

:string

Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command.

.+

tag

:string

Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command.

.+

Output

name:type
description
pattern

dataset

$prefix

:directory

Directory containing the dataset

versions_nextclade

${task.process}

:string

The process the versions were collected from

nextclade

:string

The tool name

nextclade --version 2>&1 | sed 's/.*nextclade \([^ ]*\).*/\1/'

:eval

The expression to obtain the tool version

versions_nextclade_dataset

${task.process}

:string

The process the versions were collected from

nextclade-dataset

:string

The dataset version used

grep 'tag' ${prefix}/pathogen.json | sed 's/.*tag.: .\([0-9-]\+Z\).*/\1/'

:eval

The expression to obtain the dataset version

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

nextclade

:string

The tool name

nextclade --version 2>&1 | sed 's/.*nextclade \([^ ]*\).*/\1/'

:eval

The expression to obtain the tool version

${task.process}

:string

The process the versions were collected from

nextclade-dataset

:string

The dataset version used

grep 'tag' ${prefix}/pathogen.json | sed 's/.*tag.: .\([0-9-]\+Z\).*/\1/'

:eval

The expression to obtain the dataset version

Tools

nextclade
MIT

SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks

github.com/nextstrain/nextclade
included in
viralrecon
maintainers
Github user antunderwood
Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub