This repository contains a list of pipelines in IRIDA available as plugins.

The IRIDA group does not maintain these plugins so any questions or concerns should be directed to the plugin's developers.

Installation

To install each of these plugins, please download the appopriate JAR file from the Release link and copy to the directory /etc/irida/plugins/ on a machine running IRIDA. Then, re-start IRIDA and you should see the pipeline appear in your list of pipelines.

Please see the IRIDA Pipeline Plugin documentation for more details.

Plugins

Name	Repository	Description	Release
Example Plugin	https://github.com/phac-nml/irida-plugin-example	An Example plugin to be used as a template for developing IRIDA pipeline plugins.
AMR Detection	https://github.com/phac-nml/irida-plugin-amr-detection	A pipeline for the detection of antimicrobial resistance genes in bacterial isolates.
ECTYPER	https://github.com/phac-nml/irida-plugin-ectyper	A pipeline to in silico serotype E.coli isolates
MLST	https://github.com/public-health-bioinformatics/irida-plugin-mlst	A pipeline for traditional MLST using PubMLST schemas.
QI-TAXON	https://github.com/quadram-institute-bioscience/irida-plugin-qi-taxon	A pipeline for read based taxon classification.
QI-PHYLO	https://github.com/quadram-institute-bioscience/irida-plugin-qi-phylo	A pipeline for rFast phylogeny pipeline (Snippy, IQTree)
Species Abundance	https://github.com/public-health-bioinformatics/irida-plugin-species-abundance	Estimate relative species abundance with Kraken2 & bracken
Resistance Screen	https://github.com/public-health-bioinformatics/irida-plugin-resistance-screen	Detect presence of specific resistance genes
TETyper	https://github.com/public-health-bioinformatics/irida-plugin-tetyper	Determine sequence types for specific transposable elements
Snippy Single	https://github.com/public-health-bioinformatics/irida-plugin-snippy-single	Variant calling against a reference genome for a single isolate
MiCall-Lite	https://github.com/public-health-bioinformatics/irida-plugin-micall-lite	Human RNA Virus Genotyping
Plasmid Screen	https://github.com/public-health-bioinformatics/irida-plugin-plasmid-screen	Locate resistance genes on plasmids
TBProfiler	https://github.com/public-health-bioinformatics/irida-plugin-tbprofiler	Identify lineage and drug resistance variants in M. tuberculosis
Snippy Phylogenomics	https://github.com/public-health-bioinformatics/irida-plugin-snippy-phylogenomics	Variant calling and core genome alignment with Snippy, phylogenetic tree reconstruction with IQTREE
SISTR	https://github.com/phac-nml/irida-plugin-sistr	The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies
COMBAT-TB: M. tuberculosis sample report	https://github.com/COMBAT-TB/irida-plugin-tb-sample-report	Report on variants and drug resistance in M. tuberculosis samples using TBProfiler and the COMBAT-TB eXplorer
COMBAT-TB: M. tuberculosis phylogeny	https://github.com/COMBAT-TB/irida-plugin-tb-phylogeny	Compute phylogeny from set of M. tuberculosis samples

Development

To develop a new plugin, please refer to the IRIDA Pipeline Plugin documentation in IRIDA and the IRIDA Example Plugin or existing plugins listed above.

Contributing

We welcome the contribution of any pipelines you have developed for IRIDA. If you wish to include this pipeline in the list, please submit a Pull Request to this repository which adds a new entry to the table in the Plugins section. This will be in the format of:

| [NAME] | [REPOSITORY/URL] | [DESCRIPTION] | [RELEASE] |

The [RELEASE] could be a direct link to your GitHub releases page (e.g., https://github.com/phac-nml/irida-plugin-amr-detection/releases), a link to the appropriate JAR file, or if you wish to make use of a badge for your release/repository, you can refer to https://shields.io/category/version.

License

Text in this repository is licensed under the Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ license. Licenses for each IRIDA plugin are specific to each plugin and should be available from the respective code repositories.