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`

`versions.yml:file`

File containing software versions

versions.yml

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

versions.yml:file

Tools

nextclade MIT

`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`

`versions.yml:file`

nextclade
MIT