BioLockJ is designed find all problems in one sitting. Every module includes a check dependencies method, which quickly detects issues that would cause an error during execution. This is run for all modules in a pipeline before the first module executes.

When BioLockJ runs, it has three major phases:

• pipeline formation - string together the modues specified in the config file along with any additional modules that the program adds on the users behalf; and initiate the utilities needed for the pipeline (such as docker, metadata, determine input type).
• check dependencies - scan the pipeline for anything that may cause an error during execution
• run pipeline - execute each module in the sequence.

Precheck a pipeline#

By including the --precheck-only argument (or -p) when running biolockj; you are running in precheck mode. BioLockJ will do the first two phases, and then stop. This allows you to quickly test changes to your pipeline configuration without actually running a pipeline. It also allows you to see any modules that are automatically added to your pipeline.