Heads up! The upcoming version 29 of Cromwell will include a breaking change in the command line syntax. Full details will be provided in the release notes when Cromwell 29 is ready for primetime; in the meantime the gist is that we're moving away from positional inputs in favor of explicit arguments. So for example this simple execution command:

java -jar Cromwell.jar run myWorkflow.wdl myWorkflow_inputs.json

will change to the more explicit:

java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json

The code changes can be viewed here for those who are into that level of detail.

We plan to update usage examples and relevant instructions in the WDL documentation materials at the time the new version is released, and will add a note regarding versions where appropriate for anyone still using a version anterior to 29. Note that there may be a short lag between the release and the documentation updates; we'll try to keep it to a minimum.



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@awscloud @BroadGenomics Jamie the Cromwell pig runs on AWS Batch! Read the blog post by @RuchMunsh at… https://t.co/n6AK77ljQo
1 Oct 18
@sminot @iprophage Tadaaa Cromwell is now on AWS, see https://t.co/gT0KFnmGC5 and https://t.co/375wew4Alk
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@sminot @iprophage Like seriously we’re talking days on a scale that a preschooler can count to. Keep an eye on the… https://t.co/JFGyviqGSL
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@sminot @iprophage Coming sooooon...
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@vanilla Aaand we're back; everything should be working properly now.
20 Sep 18

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@sminot So true! If the workflow manager side of you is interested, check this out. I’ve been getting more into thi… https://t.co/GmXZKac9b5
21 Sep 18
We had a lot of fun in the last day of the #GATK workshop. A lot to learn and practice on their workflow descriptiv… https://t.co/bTMSyT8W60
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Today at #GATK course, pipelining with WDL, Cromwell and Firecloud! @ClinicalBioinfo @FProgresoysalud @gatk_dev https://t.co/V4bLinpoPh
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Pretty cool. An #rstats shiny dashboard for Cromwell (and thus both #OpenWDL and #commonwl) https://t.co/Qg9ZBa1slX
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