Option to provide credentials JSON to access CRAMs & fix bug in Whamg #333
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mwalker174
reviewed
Apr 13, 2022
wdl/CramToBam.wdl
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| runtime_attr_override = runtime_attr_localize_cram | ||
| } | ||
| } | ||
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| if (requester_pays) { |
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Suggested change
| if (requester_pays) { | |
| if (requester_pays && !defined(service_account_json)) { |
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If the cram is in a requester pays bucket, I think it would fail before this point because there is no billing project provided to the gsutil cp command in the localization task
wdl/Utils.wdl
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| RuntimeAttr default_attr = object { | ||
| cpu_cores: 1, | ||
| mem_gb: 3.75, |
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Is 3.75 optimal? Can you use 0.9?
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Just tested and LocalizeCram completed successfully with 0.9GB memory on a new sample with a similar runtime, so seems fine to set that as default
mwalker174
approved these changes
Apr 13, 2022
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Updates
String? service_account_jsoninput toGatherSampleEvidence. If provided,CramToBamwill use the credentials JSON to access and localize the CRAM prior to converting to BAM. This is done in a separate task because the disk size cannot be estimated without access to the CRAM, so the localization task should be as short as possible, and then the regularRunCramToBamtask can use dynamically-allocated resources. This input was not added to any test JSONs as it is not the default behavior.Whamgbug from gatk-sv-single-sample workflow (v.0.9.1-beta-hotfix) failing at RunWhamgIncludelist subtask #332. The file/sys/fs/cgroup/memory/memory.statno longer exists, possibly due to a change to GCE VMs. The comment suggests it was only accessed for debugging purposes, so the line was deleted to prevent the error.Testing
GatherSampleEvidence(includingCramToBamandWhamg) on one sample with aservice_account_jsonrequired to access the CRAM file. Also ran on one sample without theservice_account_jsonto make sure that typical processing is unaffected, andCramToBamcompleted successfully.