How to use Directory type as defined in WDL development spec
Attempting to use the Directory keyword as defined in WDL development spec:
I execute the following command with the Cromwell v54 jar:
- java -jar cromwell-54.jar run test-inputs.wdl --inputs test.inputs.json
and receive the following error:
ERROR: Unexpected symbol (line 2, col 5) when parsing '_gen10'.
Expected rbrace, got Directory.
Directory inputs_path
^
$workflow = :workflow :identifier :lbrace $_gen10 :rbrace -> Workflow( name=$1, body=$3 )
Does cromwell currently support the Directory type? I see the following on the language support page:
https://cromwell.readthedocs.io/en/stable/LanguageSupport/
Future Language Support
WDL 'development'
As the SPEC is being improved and honed, Cromwell continues to support the current development version of WDL. That means that when (or shortly after) new versions are published, Cromwell will be ready to support them.
My use case is I am attempting to run a dockerized version of Illumina bcl2fastq. I need to pass in the entire run directory to the container.
FWIW I am not sure if this is the correct forum to post this question. I found this page from the getting help section of the Cromwell docs: https://cromwell.readthedocs.io/en/stable/GettingHelp/
Thank you for your time.
-
Hi Matthew Galvin,
Our GATK support team is focused on GATK specific questions and questions regarding GATK abnormal results. Here is our support policy for more information. You can leave this post here in case other users can provide insight and you can also check out these resources for more information:
- Mailing list for general conversation with the WDL community
- Github issues for suggestions and WDL issues
- Slack for real time chat with other community members
- Stack Overflow for asking questions about writing and using WDL
- WDL docs:
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