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:bug:
### :pencil: Describe the Issue
I just found some docs that are linking to PHBG instead of PHB WDL code. These need to be updated. One example:
https://github.com/theiagen/public_health…
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To-be-addressed from https://github.com/talkowski-lab/gatk-sv-v1/pull/252:
> * Some workflows currently require index files as inputs (e.g. module00c/CNMOPS). They should either be given default va…
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[This script](https://github.com/broadinstitute/gatk-sv/blob/master/src/sv-pipeline/04_variant_resolution/scripts/process_posthoc_cpx_depth_regenotyping.sh) is not scaling well in larger cohorts (>10K…
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As detailed in https://github.com/dockstore/dockstore/issues/5594, some workflow engines, including miniwdl and Cromwell, fail to run a valid Dockstore workflow when:
* the workflow is referenced v…
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I tried to run pipeline on cluster without internet connection, with local docker. But this error:
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='github.com', port=443): Max retries e…
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Hello :)
I have a question regarding viral-ngs and its capabilities for detecting virus integration and outputting the results to a text file. I tried to understand the explanation provided in the …
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We want to make PharmCAT easily available on cloud genomics analysis platforms. We already publish a Docker image to Docker Hub so it should be relatively easy to make that image available to differen…
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The `disks` key in the `runtime` section is documented as providing "persistent volumes" at certain mount point paths. Those paths are specified as being "in the host environment" in WDL 1.2, and I th…
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Various QC WDL such as `QC/tasks/quast.wdl` reference their docker image dependency using the `:latest` tag. This causes an ambiguity on which image is required, as latest is an ambiguous tag (change…
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The tasks pvacseq and pvacfuse hang and eventually time out and to to a retry. This happened with a number of different samples. I was able to fix the hanging by changing back to the docker image us…