incorporate assemble_refbased as refine/polish for denovo

[dpark01]

This PR takes the latest updates of assemble_refbased in the past couple years and incorporates them (directly as a subworkflow) as the refine/polish steps of de novo assembly.

Various updates:

• assemble_refbased: add lofreq vcf outputs by default
• scaffolding: change default imputation aligner from muscle to mummer (keep it big-genome friendly by default)
• remove some vestigal WDL code
• more allowNestedInputs by default (expose subworkflow and task level optional inputs to user)
• replace polish/refine steps in assemble_denovo and scaffold_and_refine workflows with assemble_refbased as a subworkflow call

This does not currently enable scattering on multiple input bams for assemble_denovo/scaffold_and_refine, that can be for a future PR.