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Most inputs which are not discussed in the usage correspond to an option or argument for a specific tool and should be self-explanatory when compared to the relevant tool’s documentation.

If something is unclear or an option/argument is unavailable, please file an issue.

The input JSON

The inputs JSON can be generated using WOMtools as described in the WOMtools documentation. However, some of the inputs presented in this JSON file should not be used/changed. This is because certain tools have inputs which are changeable, due to the usage of reusable tasks definitions for these tools. They were defined in this manner to allow for the task to be used in different workflows and different situations. In some cases, though, a specific workflow requires specific values to be given to some of these options.

Please do not use the following inputs:

• pipeline.config.sample
• pipeline.config.library
• pipeline.config.readgroup
• pipeline.sample.config.library
• pipeline.sample.config.readgroup
• pipeline.sample.library.config.readgroup

DISCLAIMER: Some inputs may have been missed in this list.

Precommands

Many tasks have a preCommand input available. This is an input which can be used to execute some bash code before a tool is run. This could be used to, for example, activate a Conda environment before running a certain job.

Java tasks

JARs

Java tools will have a JAR input available which can be used to set the location of the JAR file for a certain tool. If this input is not given the assumption is made that a Conda environment is used in which the tool is installed and the tool can be run without explicitly calling java. eg. picard will be run as picard -Xmx4G ..., rather than java -Xmx4G -jar <picardJar> ...

Memory and memory multiplier

Java tools will have a memory and memoryMultiplier input available. The first can be used to set the value given to java’s -Xmx option. The second is used to determine the actual runtime memory setting, which will equal memory * memoryMultiplier.