openwdl / learn-wdl Goto Github PK

Thank you for creating the amazing learn WDL tutorial. There are two typos in two cromwell setup commands (learn-wdl/5_reference_material/2_WDL-dev-env.md). The broadinstitute was misspelled into broadinstutite. Thus those commands are not working. Please update those commands into:
curl -L -o cromwell-50.jar https://github.com/broadinstitute/cromwell/releases/download/50/cromwell-50.jar
curl -L -o womtool-50.jar https://github.com/broadinstitute/cromwell/releases/download/50/womtool-50.jar

I'm encountering an error while working with a WDL (Workflow Description Language) script. The error message is as follows:

```ERROR: Unexpected symbol (line 8, col 5) when parsing 'setter'.

Expected equal, got "command ".

command {
^
$setter = :equal $e -> $1 ```

The issue seems to be related to the command block within one of the tasks in my WDL script. I'm not sure what's causing this error, and I would appreciate any guidance on how to resolve it.

Here's the relevant portion of the WDL script:

  ``` task CreateOutputDirectory {
      File outputDir
      
      # Input block for the task.
      input {
          File outputDir
      }
      
      command {
          mkdir -p ~{outputDir}  
      }
      
      output {
          File createdOutputDir = "~{outputDir}"  # Define the created output directory as an output.
      }
  } ```

Could someone please help me understand what's causing this error and how to correct it? Your assistance would be greatly appreciated.
I tried " command <<< >>>" method also.

I wrote this script using WDL docs tutorial and this github
https://docs.openwdl.org/en/latest/WDL)

add option to use GitHub codespaces to run WDL files

Hi,

Is there a way to use arbitrary environment variables in WDL? If so, what's the syntax? For example, how would you read and set an environment variable?

Regards,