staphscan
Tags: staphylococcus-aureus surveillance mlst spa-typing sccmec amr virulence sample-scope
Genome-based surveillance analysis of Staphylococcus aureus.
This subworkflow uses StaphSCAN to perform genome-based surveillance of Staphylococcus aureus, integrating species identification, MLST, spa typing, SCCmec typing, capsular typing, and detection of virulence, biofilm, and antimicrobial resistance genes. It processes each sample individually and aggregates the results into a single consolidated report.
Take
fna: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | Assembled contigs in FASTA format |
db: Path?
| Name | Type | Description |
|---|---|---|
db | Path? | Custom MLST database directory |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Per-sample surveillance summary with MLST, spa type, SCCmec, capsule, AGR, resistance, biofilm, and virulence results |
run_outputs
| Output | Description |
|---|---|
csv | A merged TSV file with staphscan results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- staphscan - Genome-based surveillance analysis of Staphylococcus aureus.
Used By
This subworkflow is used by the following workflows:
- staphscan - Genome-based surveillance analysis of Staphylococcus aureus.
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) -
StaphSCAN
Bollini R StaphSCAN (v0.3.0). Zenodo (2026)