5. Using junifer

In this section, we will cover the main aspects behind using junifer. We will first explain the basics behind junifer’s code-less configuration. Then we will show how to use the command line interface to run the pipeline and collect the results. Finally, we will show how to use the queue command to interact with HPC and HTC systems.

Contents:

• 5.1. Code-less Configuration
  • 5.1.1. General Parameters
  • 5.1.2. Step-by-step Configuration
  • 5.1.3. Complete Example
• 5.2. Running Jobs
  • 5.2.1. Example of running two elements:
  • 5.2.2. Example of elements with multiple parameters and verbose output:
• 5.3. Collecting Results
• 5.4. Queueing Jobs (HPC, HTC)
  • 5.4.1. HTCondor
  • 5.4.2. GNUParallelLocal

5.5. Using Common Components

The following sections explains common components of junifer that can be used across many steps of the pipeline.

Contents:

• 5.5.1. Masks