cwhelan
cwhelan
As discussed in https://github.com/broadinstitute/cromwell/issues/6235, developers of workflows for GCP who store their images in Google Container Repositories can be exposed to large Google GCS egress charges when users attempt to...
The definition for m2.xlarge in `org.jclouds.ec2.compute.domain.EC2HardwareBuilder` has a single 420GB Volume that is also the boot drive. ``` java /** * @see InstanceType#M2_XLARGE */ public static EC2HardwareBuilder m2_xlarge() { return...
I've been trying to develop an EMA processing pipeline using Cromwell and WDL with a Google Compute Engine backend. This involves switching a lot of the multithreaded parallelism you illustrate...
During the course of working on https://github.com/broadinstitute/gatk-sv/issues/520 I noticed what looks like a possible logic/processing error in `src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh`. The script starts by creating a bed file from the input VCF:...
A user has run into an error in in the single sample pipeline, version 0.26.9-beta, involving a failure of one shard of the `IntegrateGQUnder5kb` task in `GenotypePESRPart2`. The task failed...
There seem to be a number of duplicated records in the final VCF output from the single sample pipeline, particularly for CPX and INV events.
Dockstore has a new workflow for GitHub workflow integration using a GitHub App which they recommend migrating to: https://docs.dockstore.org/en/stable/getting-started/github-apps/migrating-workflows-to-github-apps.html The main advantage of switching over to this that I can...
More feedback from clinical users: The pipeline currently annotates variants with the overall AF in gnomAD and the AF in each continental subgroup. It would be helpful to provide an...
In https://github.com/broadinstitute/gatk-sv/pull/96, @epiercehoffman suggested: > Finally, I do have some worries about template files piling up once we do a similar thing for the Terra cohort pipeline, as it looks...
On single sample pipeline runs for which the gCNV workflow should be cached, gCNVCase.PostprocessGermlineCNVCalls takes more than an hour to get past on Cromwell - 1 hour and 21 minutes...