merlin_dist

Tags: merlin mash routing logic genus-specific automation sample-scope

Identify species to trigger genus-specific downstream analyses (Merlin).

This is a specialized process for the Merlin workflow. It runs mash dist against a reference database and parses the results to detect specific genera (e.g., Salmonella, Staphylococcus). Based on the detected genus, it outputs data into specific channels to trigger targeted tools (e.g., finding Salmonella triggers Sistr).

Inputs

record (
    meta: Record,
    fna: Path,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

reference: Path

Name	Type	Description
reference	Path	The reference Mash database to screen against

Outputs

record (
    meta: Record,
    fna: Path,
    r1: Path,
    r2: Path,
    se: Path,
    lr: Path,
    escherichia: Path?,
    haemophilus: Path?,
    klebsiella: Path?,
    legionella: Path?,
    listeria: Path?,
    mycobacterium: Path?,
    neisseria: Path?,
    pseudomonas: Path?,
    salmonella: Path?,
    staphylococcus: Path?,
    streptococcus: Path?,
    genus: Set<Path?>,
    dist: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
fna	Path	Passthrough of assembled contigs
r1	Path	Passthrough of Illumina R1 reads
r2	Path	Passthrough of Illumina R2 reads
se	Path	Passthrough of single-end reads
lr	Path	Passthrough of long reads
escherichia	Path?	Conditional marker file triggering Escherichia analysis tools
haemophilus	Path?	Conditional marker file triggering Haemophilus analysis tools
klebsiella	Path?	Conditional marker file triggering Klebsiella analysis tools
legionella	Path?	Conditional marker file triggering Legionella analysis tools
listeria	Path?	Conditional marker file triggering Listeria analysis tools
mycobacterium	Path?	Conditional marker file triggering Mycobacterium analysis tools
neisseria	Path?	Conditional marker file triggering Neisseria analysis tools
pseudomonas	Path?	Conditional marker file triggering Pseudomonas analysis tools
salmonella	Path?	Conditional marker file triggering Salmonella analysis tools
staphylococcus	Path?	Conditional marker file triggering Staphylococcus analysis tools
streptococcus	Path?	Conditional marker file triggering Streptococcus analysis tools
genus	Set<Path?>	Marker file indicating the detected genus
dist	Path	Raw Mash distance results
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

mashdist Parameters

Parameter	Type	Default	Description
--mash_sketch	string		The reference sequence as a Mash Sketch (.msh file)
--full_merlin	boolean	false	Go full Merlin and run all species-specific tools, no matter the Mash distance

Used By

Subworkflows

• merlindist - Identify species from assembly and read data using Mash distances.

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)

• Mash
  Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016)

• NCBI RefSeq Database
  O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O0, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733-45 (2016)

Source

View source on GitHub

Version

MERLIN_DIST:
    - mash: 2.3