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WDL | Add Variables

Add Variables


In this context, variables are placeholders that we write into the script instead of actual filenames and parameter values. We can then specify the filenames and values we want to use at runtime (meaning when we run the script) without modifying the script at all, which is very convenient. We don't have to use variables for everything, mind you -- for some parameters it makes sense to hardcode the values if they're never going to change from run to run.

So let's look at how to include variables in our WDL script (we'll talk later about how to specify variable values at runtime). There are two different levels at which we might want to include variables: within an individual task, or at the level of the whole workflow, so that the variables will be available to any of the tasks that it calls. We'll start with task-level variables because it's the simplest case, then build on that to approach workflow-level variables, which come with a few (very reasonable and totally not hard) complications. In the course of this explanation we'll touch on how variable values can be inherited from one task to the next, which is a sort of preview for the next topic, on connecting tasks together.


Task-level variables

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Adding task-level variables


Going back to task_A from our earlier example, let's look at what it actually contains in its command and output component blocks. We made up an imaginary program called do_stuff which presumably does something more interesting than printing "Hello World". This program requires two files to be provided with the arguments R= and I=, respectively, and produces an output file that must be named using the argument O=. If we were to hardcode the values, we could just write the command line as we would run it in the terminal, e.g. do_stuff R=reference.fa I=input.bam O=variants.vcf.

To replace these hardcoded values by variables, we first have to declare the variables, which is a fancy way of saying we write their name and what type of value they stand for at the top of the task block, as in e.g. File ref. Then we can insert the variable name within the command, at the appropriate place, within curly braces and prefaced by a dollar sign, as in e.g. R=${ref}.

Here for the value of O= we use the variable to specify only a base name. The script will automagically concatenate this base name with the .ext file extension that we hardcoded, producing the complete output file name from ${id}.ext.

Finally, we identify any arguments of the command that we want to track as program outputs (in this case, the O= argument) and declare them by copying their assigned contents to the output block as shown in the example. Notice that here too we specify the variable type explicitly.


Workflow-level variables

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Adding workflow-level variables


Moving one level out, to the body of the workflow, you see that we have now also declared a set of variables at the top. These declarations follow essentially the same rules as those inside a task. All we need to do now is connect these two levels, so that arguments passed to the workflow can be used as inputs to the task.

To do so, we simply add a code block to the call function. This block simply contains an input: line that enumerates which workflow-level variables connect to which task-level variables.

We do something very similar for the second task that we're calling in this workflow, task_B, with a key difference. First, the common part: task_B also takes in the reference file as input, so we can simply feed the same workflow-level variable, my_ref. to the corresponding variable in task_B. However, for its other input we need to give task_B the output of task_A. Conveniently, we can simply refer to that using a task_name.output_variable syntax -- so in this case, task_A.out.

Finally, we still need to know how to pass values to the workflow to populate all of those variables, don't we? Yes. Yes we do.

You could hardcode the values when you declare the variables, of course, and for some parameters that you know will always be the same, it makes sense to do it that way. But there are certainly some variables that you need to keep, well, variable, so you don't have to edit your script from run to run.

How that is done in practice is mostly up to the execution engine, not WDL. Pipelining systems typically use one of two main strategies to fulfill this need: either provide the values as part of the command line that launches the workflow execution, or provide a sort of configuration file that lists all the desired values. In the Cromwell execution engine we prefer to use a file of input definitions, as detailed in a later section.


Well that wasn't so bad. In the next section, we'll look at how we can connect tasks through their inputs and outputs, plus some additional functions, to produce full-featured without unnecessary code complexity.


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