Extend functionality for outlier sample exclusion workflow

[RCollins13]

This PR extends the existing outlier sample exclusion workflow, wdl/FilterOutlierSamples.wdl, in several respects:

1. Accept one or more vcfs. This is necessary for large cohorts (e.g., gnomAD) where each chromosome is stored as a separate VCF for improved parallelization in the cloud, but we need to define outliers based on the sum of variants across all VCFs.

2. Add an optional VCF preprocessing step (with bcftools) prior to collecting sample counts. This is necessary in situations where we want to restrict to certain subsets of variants for defining outliers. Two empirical use cases from gnomAD v3 include: (a) restricting to rare (AF<1%), non-singleton (AC>1) deletions between 300bp - 1kb to deal with the artifact deletion bump we sometimes see in various callsets, and (b) restricting to PASS-only variants for defining our final set of samples at the very end of all QC & post-processing.

3. Allow outlier samples to be defined on one or more independent subsets of samples within the same VCF. This is necessary when cohorts contain a mixture of samples with different properties (e.g., PCR+ vs. PCR-) and we want to fit their SV count distributions separately when defining outliers. These are optional inputs to the workflow; if no values of sample_subset_prefixes and sample_subset_lists are provided, then outliers will be defined for all samples in the VCF together.

4. Enable (optional) plotting of outlier distributions from within the workflow. I understand that there is a separate workflow for plotting outlier distributions (PlotSVCountsPerSample.wdl) and the intention is for users to optionally run that workflow after collecting per-sample counts, but from a convenience perspective I thought it would be useful to have plotting as an option of the main outlier workflow. If there is a design reason why this is undesirable, we can remove the plotting, but I know I have enjoyed having this convenience added for gnomAD.

I have tested the above changes on gnomAD v3 (24 VCFs & ~120k samples) and can confirm that they work as expected. I have not tested a cohort with a single VCF but I believe it should work as long as the VCF is passed as an array of one element.

[VJalili]

Thanks @RCollins13! Could you please undo the changes to the dockers.json file? Docker images will be rebuilt as needed and the new images will be added to dockers.json automatically as part of the CI/CD when this PR is merged.

[RCollins13]

Thanks for pointing that out, @VJalili! This made me realize I had rebased versus the old master branch before submitting this PR, so I just pulled the main branch and rebased this PR versus the main. That should have reverted all of the changes to dockers.json but let me know if anything else looks odd!

[VJalili]

Thanks, @RCollins13, that looks great.

[VJalili]

@RCollins13 if you rebase your branch on the latest main, some errors in the Test WDLs action should be resolved.