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### Feature Request
This issue is a solicitation for feedback on an idea.
I've been working on the [RSV pipeline](https://github.com/CDPHE-bioinformatics/CDPHE-RSV) and reusing tasks from this r…
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Hello,
I am trying to run the SHARE-Seq pipeline starting from the preprocessing step on an HPC.
- Could someone share an example JSON and other required preprocessing files for starting the ana…
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### Feature Request
We are reaching our CPU limit for our production Terra workspace. This is negatively impacting our pipeline and preventing us from reliably meeting dashboard updates.
This is…
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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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In several cases in the workflow repository we are not outputting the stats file needed in order for the nmdc_automation code populate mongo records with workflow specific fields (ie contig_bp for nmd…
aclum updated
3 weeks ago
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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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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 TSV spit out by the decontam task is different based on the decontamination reference genome that gets used. Currently, when the CRyPTIC reference is used, the wrong thing happens.
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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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I'm running a workflow like this:
```
MINIWDL__CALL_CACHE__GET=true MINIWDL__CALL_CACHE__PUT=true MINIWDL__CALL_CACHE__DIR=`pwd`/output/miniwdl-cache MINIWDL__SCHEDULER__TASK_CONCURRENCY=80 time min…