First pass top-down work, mostly from Friday.

Simplify generate_result. Move all validation to one method. Move all workflow input generation to one method. Use Build clumps.
work so far!
remove unnecessary module
First pass top-down work, mostly from Friday.

Simplify generate_result. Move all validation to one method. Move all workflow input generation to one method. Use Build clumps.
work so far!
Add CreateRegionFile to ccsvcf

This lets us only convert the segregating_sites_vcf_file one time before
the parallel-by BackfillVcf step.
Add Pileup and Backfill to ccsvcf

These commands just wrap some other gmt commands so they can take
'build_clump's as inputs.  They're used in the BackfillVcf step of
create-crosss-sample-vcf for snvs.
Added xml to describe ccsvcf for snvs with region limiting
Added xml to describe ccsvcf for indels with region limiting
Fix typo
Add FIXME
Added RegionLimitVcf to ccsvcf

It is just a wrapper around RegionLimit which allows it to take a build
as an input.
Added processing_profile option to gmb validate
Added get_detectors method to dv2 strategy

This allows us to not parse the strategy string by hand in
CreateCrossSampleVcf.
Fix parallelBy syntax
Make region file a gzip file and allow case of no alts
Fix typo backfill(ed)
CreateCrossSampleVcf overhaul for snvs

We now use a single workflow xml file with parallelBy so that this will
scale with ptero, and so that the snvs and indels code can be shared as
much as possible.
use same max_files_per_merge in both tests
Ensure max_files_per_merge is being set

This was missing from the xml, setting it made it apparent that we need
two working directories (one for the initial merge and another for the
final merge).