Use GATK tool SVAnnotate for functional consequence annotation

[epiercehoffman]

Updates

Replace svtk annotate with GATK tool SVAnnotate for functional consequence annotation during AnnotateVcf.wdl.

• Create standalone workflow AnnotateFunctionalConsequences.wdl that runs SVAnnotate with a protein-coding GTF and optionally a BED file of noncoding elements, with optional tool parameters exposed.
• Call AnnotateFunctionalConsequences as a subworkflow during AnnotateVcf.wdl. Scattering should not be necessary for a small / medium sized cohort as SVAnnotate runs in ~25-30 mins on an unfiltered VCF with ~2500 samples, so scattering was not implemented, but it may need to be run separately per contig for very large cohorts.
• Update single-sample WDL as needed
• Update JSON & Terra templates as needed
• Remove old annotation WDLs
• Change custom canonical protein-coding GTF to MANE Select Plus Clinical GTF

Testing

• Ran AnnotateVcf.wdl successfully with 1KG ref panel with cromshell
• Validated all WDLs and JSONs with womtool (decrease to 27 test JSONs) & Terra validation script

[mwalker174]

Great work! Always happy to net 800 fewer lines and simplify the WDLs while fixing bugs and improving performance! A couple of minor suggestions.

Just checking: does the GATK docker need to be updated in dockers.json?

[mwalker174]

Suggested change

	~{if defined(noncoding_bed) then "--non-coding-bed " + noncoding_bed else ""} \
	~{"--non-coding-bed " + noncoding_bed} \

Same for the others. Unless there was a miniwdl issue with this?

[epiercehoffman]

I don't think this was the issue with miniwdl

[mwalker174]

What do you think about adding an String additional_args input that would let the user specify arbitrary arguments not built into the wdl (e.g. a requester pays project id)?

[epiercehoffman]

Just checking: does the GATK docker need to be updated in dockers.json?

No, the current gatk_docker (the nightly snapshot) has SVAnnotate and that's what I used for testing.

Updated the way optional arguments are handled, added an optional additional_args parameter, validated with womtool, and tested successfully with default inputs (did not try with providing additional_args).