more scaffolding updates

[dpark01]

scaffold_and_refine_multitaxa:

• more resilience to empty outputs or partial recovery of multi-segment genomes
• update input reference genome data structure to tsv instead of json string
• auto-filter input reference genome list (optionally) based on kraken hits
• run polish only if scaffolding successful--if not successful, fallback to refbased assembly as hail mary attempt
• more top-level (terra table) outputs

classify_single:

• more top-level workflow outputs summarizing primary viral taxa found, and how much

containers:

• bump viral-classify 2.2.3.0 to 2.2.4.0

build:

• update cromwell/womtool version