gigatyper

Tags: mlst typing multi-scheme sample-scope

Run all available MLST schemes for a species against an assembly

Uses GigaTyper to run all available mlst schemes for a species against an assembly.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	MLST results across all schemes
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

GigaTyper Parameters

Parameter	Type	Default	Description
--gigatyper_species	string		Force a specific species for scheme selection

Used By

Subworkflows

• gigatyper - Run all available MLST schemes for a species against an assembly

Workflows

• gigatyper - Run all available MLST schemes for a species against an assembly

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• GigaTyper
  Petit III RA, Fearing T, Groves E GigaTyper: Why choose one scheme when you can flex them all? (GitHub)

Source

View source on GitHub

Version

GIGATYPER:
    - gigatyper: 1.0.0