improvements to sarscov2_illumina_full

[dpark01]

• bugfix: bump viral-assemble from 2.1.16.0 to 2.1.16.1 (fix behavior on empty input)
• expose sarscov2_illumina_full properly on dockstore
• rename sample ids at the beginning prior to demux in both sarscov2_illumina_full and demux_deplete
• fix sample metadata map under cromwell/terra (use read_json instead of read_map)
• add gisaid fasta output
• add metric for worst NTC
• align_and_count now names the single biggest spike in for each sample
• more sample and library metadata emitted in json and/or structured format for downstream decoding