nextstrain wdl updates

[dpark01]

In this PR:

• rename build_augur_tree to augur_from_assemblies to be more consistent with the other workflows that are named augur_from_*. -- beware downstream effects on Dockstore
• bugfix travis build on augur_from_beast
• some VM shape tuning on nextstrain tasks
• some more CPU/RAM profiling/output on nextstrain tasks
• some more automatic output filename determination (based on input filenames) so we ask for it less in task inputs
• bugfix: invocation of snp-sites should always have a -c or else the VCF will be polluted with * characters and won't be a valid VCF file