WDL workflow inputs#
It is easy to specify (hard-code) file paths and parameter values for the workflow input variables directly in your WDL scripts. However, this practice undermines the code integrity and reproducibility of setting up a production workflow in the first place. Instead, we recommend using a JSON file to define all the variable values for file and parameter inputs which you can then customize for each run without having to modify your WDL workflow scripts. The Cromwell execution engine will then use the JSON file to fill in the input values of your task commands whenever applicable.
You can use the Cromwell open source package () to simplify the process of generating the JSON skeleton file of workflow inputs. The package comes with a set of command line utilities (WOMtool) for interacting with the Workflow Object Model (WOM), including a utility that parses your WDL workflow scripts and generates the input JSON skeleton file. For details, see Create an input JSON file.