v2.1.0.4

assemble_refbased workflow:

• default to minimap2 aligner instead of novoalign [#123, #110]
• add run_discordance task and output metrics for measuring discordance between sequencing runs within a sample [#124]
• disable ivar trim quality trimming due to unidirectional trim behavior (only run ivar trim for PCR primers) [#122]
• remove MultiQC from refbased workflow [#82]

metagenomics:

• bugfixes for kraken2 build [#120, #117]
• bugfixes for kaiju task [#113]
• remove blastx (optional) tasks from classify_multi [#102, #106]

BEAST (GPU):

• increase dnanexus runtime limit and specify dx_instance type [#116, #118]
• update docker image [#111]

nextstrain / phylogenetics:

• add snp-sites task to emit vcf files [#115]
• add augur mask step [#99]
• VM shape tuning [#112]
• rename and reorganize workflows a bit so they are all called augur_from_xxx [#121, #101]

miscellaneous:

• demux workflows: append lane number to bam filenames [#98, #100]
• update viral-core [#105, #124]
• update dxWDL [#103]