Automating Analysis Workflow
How do I batch (apply to multiple inputs) a workflow that I created on the DNAnexus website?
The DNAnexus SDK provides a few dedicated utilities useful for batch processing. Please, check the Running Batch Jobs Tutorial for more information on how to run a workflow or an application on many inputs automatically.
Alternatively, you can use the
dx run command to achieve this goal. For example, if you create a workflow called "Trio Exome Workflow - Jan 1st 2020 9:00am" in your project, you can run it from the command line in this way:1
dx login
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dx run "Trio Exome Workflow - Jan 1st 2020 9\:00am"
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Note the
\ that is needed to escape the : in the workflow name.Inputs to the workflow can be specified using
dx run <workflow> --input name=stage_id:value, where stage_id is a numeric ID starting at 0. More help can be found by running the commands dx run --help and dx run <workflow> --help.Batching of multiple inputs can then be done like this:
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dx cd /path/to/inputs
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for i in $(dx ls); do
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dx run "Trio Exome Workflow - Jan 1st 2020 9\:00am" --input 0.reads="$i"
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done
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Last modified 2yr ago
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