sarscov2 workflow updates

[dpark01]

• new workflow: sarscov2_sra_to_genbank -- this takes sequencing reads from INSDC (via NCBI SRA), assembles, annotates, and QCs genomes, and produces Genbank and GISAID submission bundles based on the metadata in NCBI (SRA and BioSample). The Genbank submission will be tied to the same source BioProject and BioSamples that the reads were linked to in SRA. This workflow is able to merge together multiple read sets (SRA records) from the same BioSample and produce one assembly per BioSample. It will automatically detect sequencing platform (only Illumina and Oxford Nanopore currently supported) as well as amplicon vs metagenomic library designs based on the SRA metadata, and assemble appropriately. This has been tested on Illumina reads, ONT reads, amplicon libraries, metagenomic libraries, reads submitted to NCBI SRA, and reads originally submitted to ENA and synced with NCBI.
• sarscov2_lineages and sarscov2_illumina_full: output variable name change from "pangolin_clade" to "pango_lineage" (to stay consistent with terminology used by the authors)
• sarscov2_illumina_full: replace the first several steps with an invocation of demux_deplete as a subworkflow