# 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. Check the [Running Batch Jobs Tutorial](/user/running-apps-and-workflows/running-batch-jobs.md) for more information on how to run a workflow or an application on many inputs automatically.

Alternatively, you can use the [`dx run`](/user/helpstrings-of-sdk-command-line-utilities.md#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 this way:

```shell
dx login
dx run "Trio Exome Workflow - Jan 1st 2020 9\:00am"
```

{% hint style="info" %}
The backslash `\` character is required to escape the colon `:` character in the workflow name.
{% endhint %}

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:

```shell
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"
done
```


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