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Automating Analysis Workflow
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 runcommand 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:
dx run "Trio Exome Workflow - Jan 1st 2020 9\:00am"
\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 --helpand
dx run <workflow> --help.
Batching of multiple inputs can then be done like this:
dx cd /path/to/inputs
for i in $(dx ls); do
dx run "Trio Exome Workflow - Jan 1st 2020 9\:00am" --input 0.reads="$i"