This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Problem with scatter Array[File] for intervals' bed file
I am trying to use haplotypecaller on one sample and a list of intervals in a bed file as described in your WDL file:
I am getting this error message and it seems related to the intervals:
As I understood it from your WDL script, the scatter function is generating a file for each line in the bed file and trying to relocate it, then complain that it doesn't exist.
I tried this WDL using cromwell 30.2 first then upgraded to the latest version 34 and still getting the same exact error message. I am using GATK 18.104.22.168 as well.
Thanks in advance for your help