Mark Walker

Input templates and data from 1000G need to be added for testing multi-batch runs and generating the Terra workspace.

We currently use Cromwell's monitoring log feature to troubleshoot and analyze resource usage. This approach runs a [monitoring script](https://github.com/broadinstitute/gatk-sv/blob/master/scripts/cromwell/cromwell_monitoring_script2.sh) in the background on every VM. Once the workflow is complete,...

Some commands in this wdl can be replaced with faster/more robust bcftools commands, and some commands simply need to be rewritten. See #51 for unaddressed comments.

We should publish working `RuntimeAttr` inputs for each module at different batch sizes. Note that the WDL defaults are generally for single-batch runs of ~100-200 samples. Note that batch size...

Modules 00b-0506 have multiple inputs of `Array[File]` or `File` that assume consistent sample IDs. For example, Module 01 has `manta_vcfs`, `delly_vcfs`, `wham_vcfs`, `melt_vcfs`, `del_bed`, and `dup_bed`. The sample IDs in...

These appear to be misclassified insertions, and at least some of them are called as INS by manta. Evaluations need to be done on some different solutions: 1) Upgrading [wham](https://github.com/zeeev/wham)...