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gatk/haplotypecaller-gvcf-gatk4 hangs up on Firecloud

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Hello,

The gatk/haplotypecaller-gvcf-gatk4 workflow on Firecloud starts and hangs without producing a workflow log, JES log, stderr or stdout file.

I noticed that in runtime section for each task in wdl script for this workflow it doesn't use ${} for pass in parameters.

_runtime {
docker: docker_image
memory: mem_size
disks: "local-disk " + disk_size + " HDD"
}
_
instead of

runtime {
docker: ${docker_image}
memory: ${mem_size}
disks: "local-disk " + disk_size + " HDD"
}

Is this correct?

Thank you.


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