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gatk/haplotypecaller-gvcf-gatk4 hangs up on Firecloud

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.
Tagged:
Answers
The parameters should still work using that format. Were you able to successfully run the method using the test dataset and the method configuration in the featured workspace?
Yes, I was able to run it. I see that in that workspace it is run on hg38 aligned bams. Is it possible to run Haplotype Caller method (haplotypecaller-gvcf-gatk4) on hg19 aligned bams? Method description doesn't specify it.
Yes, there is a featured workspace using the method on b37(hg19) reference data and test bam.
A workflow may slow when pulling docker images from docker hub instead of the images in Google Cloud Repository, where are you pulling your docker image from?