IRIDA Plugin builder

The build_workflow.sh script uses Docker and the quay.io/combattb/irida-builder:21.09.2 builder to build an IRIDA workflow and copy the resulting jar to the output directory as specified on the command line.

Procedure for updating an IRIDA plugin

The Galaxy workflow .ga file can be converted to a IRIDA workflow format using irida-wf-ga2xml. An example command is:

java -jar irida-wf-ga2xml-1.2.0-standalone.jar -n TBSampleReport -t VARIANT_CALLING -W 0.4.1 -o /tmp/wf -i Galaxy-Workflow.ga

This will create a /tmp/wf directory with a subdirectory named after the version number. Put the version-numbered directory in src/main/resources/workflows of your workflow repository and take note of the UUID-style <id>. Copy the ID to the relevant Java file in src/main/main/java/ca/corefacility/bioinformatics/irida/plugins and copy the version number to the pom.xml file in both the <version> and <plugin.version> fields. Note that the irida-wf-ga2xml will only create a <sequenceReadsPaired> input section in the irida_workflow.xml if you have an input of type list:paired in your Galaxy workflow. If you are using single ended input, you need to manually put a <sequenceReadsSingle> section in the irida_workflow.xml. E.g. <sequenceReadsSingle>input_sequence</sequenceReadsSingle> where input_sequence is the label of your list type collection input for the Galaxy workflow. For more help, read the IRIDA Pipeline Development docs.

Integrating the plugin builder with your workflow repository

To integrate this into a Github repository storing an IRIDA plugin, add this repository as a submodule called build in your repository, i.e. run:

git submodule add https://github.com/COMBAT-TB/irida-plugin-builder.git build

in the top level directory of your IRIDA plugin repository. Then add a Github Action like this example. See the TB Sample Report plugin for a complete working example.

This will build a new release jar file of your workflow each time you push a tag to your Github repository.