Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Can inputs be specified on the command line?
edpark_clearlabs
Member ❠
Is there a way to specify the the values for some input variables to Cromwell on the command line rather than having to use an input JSON file?
For example, something like:
--inputs myconfig.flag=foobar
Best Answer
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danb
✭✭✭
To be more precise, no there is not a way to provide an input value via the command line
runcommand, although that does seem like a reasonable request. I created this issue in github to track it.
Answers
If you want to hardcode it, yes, just include it in your
command. If not hardcoded, ultimately your input will have to be provided via the input JSON file.To be more precise, no there is not a way to provide an input value via the command line
runcommand, although that does seem like a reasonable request. I created this issue in github to track it.https://github.com/broadinstitute/cromwell/issues/3406