Nextflow Registry | nf-core/nextclade/run@0.0.0-6c4ed3a

nf-core/nextclade/run @ 0.0.0-6c4ed3a

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

nextclade variant consensus

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @antunderwood @drpatelh

Maintainers: @antunderwood @drpatelh @drpatelh

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

Add the following snippet to your workflow script to include this module.

include { NEXTCLADE_RUN } from 'nf-core/nextclade/run'

MIT License

Process

`Name`	`NEXTCLADE_RUN`

Input 2 channels

#1 tuple

`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 11 channels

#1 csv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.csv` file	CSV file containing nextclade results `*.{csv}`

#2 nwk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.nwk` file	NWK file containing nextclade results `*.{nwk}`

#3 tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.tsv` file	TSV file containing nextclade results `*.{tsv}`

#4 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.json` file	JSON file containing nextclade results `*.{json}`

#5 ndjson tuple

`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}`

#6 versions

`versions.yml` file	File containing software versions `versions.yml`

#7 csv_errors tuple

`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}`

#8 json_auspice tuple

`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}`

#9 fasta_aligned tuple

`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}`

#10 csv_insertions tuple

`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}`

#11 fasta_translation tuple

`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.}`