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.

Coverage is likely the most important output from this subworkflow, and is dependent on the size of the genome in question. There is a json file with the expected sizes of each organism at Grandeur/assets/genome_sizes.json, which is determined by the top fastani hit. The end user can supply their own json file with params.genome_sizes or submit an issue if a genome size should be adjusted.

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Information Subworkflow
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flowchart TD
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 --> legsta
A -- if Klebsiella --> kleborate
A -- if E. coli --> serotypefinder
A -- if E. coli --> shigatyper
A -- if Salmonella --> seqsero2

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Relevant params with their default values:

params.genome_sizes           = "/path/to/genome_sizes.json"
params.amrfinderplus_options  = ""
params.emmtyper_options       = ""
params.fastqc_options         = ""
params.fastqscan_options      = ""
params.kleborate_options      = "-all"
params.legsta_options         = ""
params.mlst_options           = ""
params.pbptyper_options       = ""
params.plasmidfinder_options  = ""
params.quast_options          = ""
params.seqsero2_options       = "-m a -b mem"
params.serotypefinder_options = ""
params.shigatyper_options     = ""