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Dear GATK developers,
Thank you very much for the tool! I recently encountered an issue while running GATK gCNV, specifically with the step GermlineCNVCaller in cohort mode. I ran the workflow usin…
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**Describe the bug**
vcf-to-gds is a simple three step workflow.
1. Scattered: Turn a VCF into a GDS
1. Not scattered: Give those GDS files unique variant IDs
1. Scattered: Check those unique-var-id-…
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Cross-posted from #405
Also see discussions here:
* https://github.com/openwdl/wdl/discussions/413
* https://github.com/openwdl/wdl/discussions/407
Currently, the WDL specification provides a small…
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## Background
The Task Execution System API is a system to provide a method to quickly run [Docker based tasks](https://github.com/ga4gh/task-execution-schemas). It provides a low level foundation th…
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**Describe the bug**
`call-hiccups_input_hic` failed, apparently because GPU resources not requested. Similar situation for `call-delta`.
**OS/Platform**
- OS/Platform: Red Hat Enterprise Linux 8…
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I use `vocab.wdl` and run this:
toil-wdl-runner --jobStore=toilWorkflowRun --logDebug --clean=never --stat vocab.wdl vocab.json
I get this:
```
INFO:toil.leader:Finished toil run successfully.
I…
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Hi Mike,
One _external_ feature we're looking to implement in the upcoming DSP hackathon is collection of runtime monitoring data from individual tasks in WDL. The metrics would be reported from ea…
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Dear @mlin,
Thanks for your great work so far. I have been thinking myself about combining miniwdl and snakemake this summer and see if I can make a WDL runtime. But now it turns out you also start…
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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…