FAQ for miniwdl

miniwdl is a local runner and developer toolkit for the bioinformatics-focused Workflow Description Language (WDL).

TIP: If you are new to working with WDL workflow language, you may want to review the open source ‘learn-wdl’ course’ - link.

Also there is an embedded short course ‘learn-miniwdl’ which includes screencasts reviewing the concepts on this page in more detail - link

Common Questions

Install and verify miniwdl

  • Q: miniwdl won’t intall (or work) on my machine
    • Verify installation of Python 3.6+
    • Verify installation of Docker.
  • Q: miniwdl isn’t working on my Mac
    • Verify Docker version (17+) and user permission for Docker.
    • You’ll first need to override the TMPDIR environment variable, e.g. export TMPDIR=/tmp to allow Docker containers to mount shared working directories.
    • Please file any other issues that arise!
  • Q: the miniwdl run command won’t run my WDL workflow
    • Verify that each workflow task runs from a Docker container image.
    • Define the container image in the WDL script (task section(s)).
  • Q: what is the quickest way to verify that miniwdl is properly installed?
    • Run miniwdl --help and review the list of possible commands.

Run WDL workflow with the miniwdl run command

  • Q: what is simplest way to test running a WDL workflow on miniwdl?
    • Run miniwdl run_self_test - it includes an example workflow.
    • Verify this job returns the ok and done messages as expected.
  • Q: how can I run a quick hello.wdl WDL workflow?
    • Copy this file to your miniwdl development environment.
    • Run miniwdl run hello.wdl, there are no input parameters used in this quick test.
  • Q: Where is the job output from miniwdl job?
    • miniwdl produces workflow, task and job logs as well as task output.
    • See the folder\file structure generated for each job run for these files.
  • Q: What does miniwdl run myfile.wdl do?
    • If your WDL file defines inputs and outputs, then it prints a list of inputs and outputs and notes which inputs are required.
  • Q: How to do I assign values to input variables when I use miniwdl to run a WDL file?
    • you can assign directly on the command line, i.e. miniwdl run myfile.wdl input1=input.bam input2= input.bai, etc...
    • or you can use the --input flag and assign input values via an input.json file
  • Q: How can I get more information about job execution?
    • Run the miniwdl run myfile.wdl command
    • Use the --verbose flag
  • Q: What is the _LAST directory?
    • miniwdl generates a symbolic link _LAST pointing to the timestamped subdirectory for most recent run, and an out directory tree containing symbolic links to the output files.

Check WDL syntax with the miniwdl check command

  • Q: When I run miniwdl check myfile.wdl it doesn’t produce any output
    • Re-run the command, sometimes it takes a couple of seconds to complete the WDL file parsing
  • Q: Do I have to fix all of items listed (warnings) in the results of miniwdl check myfile.wdl
    • This command generates both warnings (which you optionally fix) and errors (which you must fix).
    • Warnings are shown in red.