rgi_heatmap
Tags: resistance antimicrobial-resistance card rgi heatmap visualization run-scope
Create heatmaps of resistance gene presence/absence.
Uses RGI (Resistance Gene Identifier) to generate heatmaps visualizing the presence or absence of antimicrobial resistance genes across multiple samples based on RGI JSON results.
Inputs
record (
meta: Record,
json: Set<Path>
)
| Field | Type | Description |
|---|---|---|
meta | Record | Groovy Record containing sample information |
json | Set<Path> | List of RGI results in JSON format |
Outputs
record (
meta: Record,
heatmap: Set<Path?>,
results: Set<Path>,
logs: Set<Path?>,
nf_logs: Set<Path>,
versions: Set<Path>
)
| Field | Type | Description |
|---|---|---|
meta | Record | Sample information record |
heatmap | Set<Path?> | Heatmap files in various formats (CSV, EPS, PNG) |
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
Used By
Subworkflows
- rgi - Predict antimicrobial resistance from protein or nucleotide data.
Workflows
- rgi - Prediction of antibiotic resistance genes using RGI.
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) -
Resistance Gene Identifier (RGI)
Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-L V, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran H-K, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research 48.D1, D517-D525 (2020)
Source
Version
RGI_HEATMAP:
- rgi: 6.0.5