modules/nextclade_run

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

nextcladevariantconsensus

https://github.com/nf-core/modules/[...]/modules/nf-core/nextclade/run

Description

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

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

FASTA file containing one or more consensus sequences

*.{fasta,fa}

`dataset`
`:directory`

Path containing the dataset files obtained by running nextclade dataset get

*

Output

name:type

description

pattern

`csv`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.csv`
`:file`

CSV file containing nextclade results

*.{csv}

`csv_errors`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.errors.csv`
`:file`

CSV file containing errors from nextclade results

*.{errors.csv}

`csv_insertions`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.insertions.csv`
`:file`

CSV file containing insertions from nextclade results

*.{insertions.csv}

`tsv`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.tsv`
`:file`

TSV file containing nextclade results

*.{tsv}

`json`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.json`
`:file`

JSON file containing nextclade results

*.{json}

`json_auspice`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.auspice.json`
`:file`

Auspice JSON V2 containing nextclade results

*.{tree.json}

`ndjson`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.ndjson`
`:file`

newline-delimited JSON file containing nextclade results

*.{ndjson}

`fasta_aligned`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.aligned.fasta`
`:file`

FASTA file containing aligned sequences from nextclade results

*.{aligned.fasta}

`fasta_translation`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_translation..fasta`
`:file`

FASTA file containing aligned peptides from nextclade results

*.{_translation.}*.{fasta}

`nwk`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.nwk`
`:file`

NWK file containing nextclade results

*.{nwk}

`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 version of the tool

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 version of the tool

Tools

nextclade
MIT

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

github.com/nextstrain/nextclade

modules/nextclade_run

Description

Input

meta:map

fasta:file

dataset:directory

Output

csv

meta:map

${prefix}.csv:file

csv_errors

meta:map

${prefix}.errors.csv:file

csv_insertions

meta:map

${prefix}.insertions.csv:file

tsv

meta:map

${prefix}.tsv:file

json

meta:map

${prefix}.json:file

json_auspice

meta:map

${prefix}.auspice.json:file

ndjson

meta:map

${prefix}.ndjson:file

fasta_aligned

meta:map

${prefix}.aligned.fasta:file

fasta_translation

meta:map

*_translation.*.fasta:file

nwk

meta:map

${prefix}.nwk:file

versions_nextclade

${task.process}:string

nextclade:string

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

Topics

versions

${task.process}:string

nextclade:string

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

Tools

nextclade MIT

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`dataset`
`:directory`

`csv`

`meta`
`:map`

`${prefix}.csv`
`:file`

`csv_errors`

`meta`
`:map`

`${prefix}.errors.csv`
`:file`

`csv_insertions`

`meta`
`:map`

`${prefix}.insertions.csv`
`:file`

`tsv`

`meta`
`:map`

`${prefix}.tsv`
`:file`

`json`

`meta`
`:map`

`${prefix}.json`
`:file`

`json_auspice`

`meta`
`:map`

`${prefix}.auspice.json`
`:file`

`ndjson`

`meta`
`:map`

`${prefix}.ndjson`
`:file`

`fasta_aligned`

`meta`
`:map`

`${prefix}.aligned.fasta`
`:file`

`fasta_translation`

`meta`
`:map`

`_translation..fasta`
`:file`

`nwk`

`meta`
`:map`

`${prefix}.nwk`
`:file`

`versions_nextclade`

`${task.process}`
`:string`

`nextclade`
`:string`

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

`versions`

`${task.process}`
`:string`

`nextclade`
`:string`

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

nextclade
MIT