Running your workflow

Now you’ve built your workflow, let’s run it on your computer.

_We’re working on a runner for engine that allows you to run your favourite workflow engine without going through this manual export process. Stay tuned for more!


In this tutorial, we’re going to run the workflow you have built with janis-runner. Behind the scenes this uses Cromwell or CWLTool to manage the execution.


To run the workflow, we’re going to use a workflow execution engine, or just engine for short. Some engines only accept certain workflow specifications, for example the CWL reference engine (cwltool) only accepts CWL, while Cromwell (developed by the Broad Institute) accepts both WDL and CWL.

What you’ll need

To complete this tutorial, you’ll need to have an installation of janis (see the Getting Started guide for more info), a workflow to run and an engine available.

Execution Engine


cwltool is the reference engine for CWL. We’d recommend visiting the install guide, however you can install cwltool through Pip by running:

pip3 install cwltool


For WDL, we’d recommend Cromwell, developed by the Broad Institute and developed alongside the openwdl community. You can find their docs here. Cromwell is packaged as a jar file, you must have a Java 8 runtime installed (ie, running java -version in the console gives you 1.8.0 or higher).

Janis will automatically download Cromwell, or it will automatically detect versions in ~/.janis/. It’s possible to configure Cromwell to run in a variety of ways through the configuration guide.


Most commonly, people use docker which both cwltool and Cromwell support by default. Some HPC friendly alternatives includesingularity and udocker; although these engines can be configured independently with both of these user-space replacements, we’re still working on an easy way to configure Janis to use these.

Let’s get started

We’re going to use the Janis command-line interface (CLI) to run these workflows and track their progress. For this example, we’re going to run the Hello workflow and put the relevant output files in an output directory called hello_dir.

By default, Janis will run the workflow using CWLTool, this can be changed by passing the --engine parameter with either "cwltool" or "cromwell".

Let’s do that now:

janis run --engine [cwltool|cromwell] -o hello_dir hello 

We’ll see some important information in our console:

  • The ID of our task. This is useful to gain access to our workflow information at a later date.
2019-09-26T00:25:00+00:00 [INFO]: Starting task with id = 'a4f047'
  • The metadata screen, this tells us about the progress of our workflow.
    • There are 3 status indicators:
      • [...]: processing
      • [~]: running
      • [✓]: completed
      • [!]: failed
TID:        a4f047
WID:        1ca1d418-df9b-45ea-b6b8-2d210be310b3
Name:       hello

Engine:     cromwell
Engine url: localhost:56232

Task Dir:   /Users/franklinmichael/janis/execution/hello/20190926_102526_a4f047/
Exec Dir:   /Users/franklinmichael/cromwell-executions/hello/1ca1d418-df9b-45ea-b6b8-2d210be310b3

Status:     Completed
Duration:   17
Start:      2019-09-26T00:25:55.771000+00:00
Finish:     2019-09-26T00:26:13.079000+00:00

    [✓] hello.hello (13s :: 76.5 %)

Finished managing task 'a4f047'. View the task outputs: file:///Users/franklinmichael/janis/execution/hello/20190926_102526_a4f047/

If we look at the contents of our output directory ($task dir + "/outputs/", eg: /Users/franklinmichael/janis/execution/hello/20190926_102526_a4f047/outputs/), we see one file called hello.out which contains the string “Hello, World!”.

Overriding workflow inputs

The hello workflow allows us to override the string that gets printed to the console. We can see in the hello documentation, there is an input called inp (optional string) that we can override.

There are two ways to override inputs in Janis:

  1. Creating a yaml job file: janis inputs hello > hello-job.yml, this file can be modified and provided to the run with --inputs hello-job.yml.
  2. Parameter overrides within the run command.

We’re going to take the second route by providing "Hello, Janis!" to the workflow:

janis run hello --inp "Hello, Janis!"

Outputting the result in the outputs folder yields:

Hello, Janis!



Congratulations on running your workflow! You can now get more advanced with the following tutorials:

Advanced arguments

CPU and Memory overrides

  • runtime_cpu: int is the number of cpus that are required.
  • runtime_memory: float is specified in number of Gigabytes.
  • runtime_disks: string is specified in the format target size type (eg: "local-disk 100 SSD")

When exporting the workflow, you have the ability to generate schema that allows you to override the cpu and memory values at a workflow inputs level. That is, you can include parameters in your input file that will ask the engine to run your workflow with specific memory and cpu requirements.

You can generate a workflow with resource overrides like so:

w.translate("cwl", with_resource_overrides=True, **other_kwargs)

You can generate an inputs file with the overrides withe following:

def generate_inputs_override(

or with the CLI:

janis inputs [--resources] > job.yaml

In CWL, this looks like:

taskname_runtime_cpu: null
taskname_runtime_memory: null
subworkflowname_task2name_runtime_cpu: null
subworkflowname_task2name_runtime_memory: null

And in WDL:

    "$name.taskname_runtime_memory": null, 			
    "$name.taskname_runtime_cpu": null,
    "$name.taskname_runtime_disks": null,
    "$name.subworkflowname_task2name_runtime_cpu": null,
    "$name.subworkflowname_task2name_runtime_cpu": null,
    "$name.subworkflowname_task2name_runtime_disks": null

Overriding export location

Default: export_path='.'

You can override the export path to a more convenient location, by providing the ``parameter to translate. Prefixing the path with ~ (tilde) will replace this per os.path.expanduser. You can also use the following placeholders (see github/janis/translation/exportpath for more information):

  • "{language}" - ‘cwl’ or ‘wdl’
  • "{name}" - Workflow identifier

You can output a workflow through the CLI with the following commmand:

janis translate [cwl|wdl] --output-dir /path/to/outputdir/