information

Serotyping and other information subworkflow

This subworkflow takes the species information from the blobtools (optional), kraken2 (optional), mash, and fastani subworkflows to set some flags for downstream species-specific processes as well as relevant processes for all samples.

---
Information Subworkflow
---
flowchart LR
Q --> fastqc
Q["fastq"] --> A
F["fasta"] --> A
blobtools .-> A["determine species"]
kraken2 .-> A
mash --> A
fastani --> A
A -- get size --> fastqscan
A -- for plus --> AMRfinderPlus
F --> quast
F --> MSLT
F --> plasmidfinder
A -- if S. pyogenes --> emmtyper
A -- if S. pneumoniae --> pbptyper
A -- if Legionella --> elgato
A -- if Klebsiella --> kleborate
A -- if E. coli --> serotypefinder
A -- if E. coli --> shigatyper
A -- if Salmonella --> seqsero2
A -- if Mycobacterium --> drprg
A -- if Mycobacterium --> mykrobe

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Please note that shigatyper is likely more useful in distinguishing E. coli from Shigella isolates than tools like mash or fastani.

Relevant params with their default values:

# to skip all these processes, set this to true
skip_extras = false
# number of mash dist hits to use for speciation estimates
params.mash_max_hits = 25