assembly and genbank updates

[dpark01]

Updates:

• All assembly processes (anything involving assemble_refbased or refine_assembly_with_aligned_reads) will now trim the edges of ambiguous bases according to a "3rules" criteria used in NCBI's VADR script "fasta-trim-terminal-ambigs.pl". This is to satisfy submission requirements enforced by table2asn which fail sequences with too much ambiguous content at the edges.
• When downloading reference genomes in scaffold_and_refine_multitaxa, save them in files that use dashes instead of colons as delimiters in the filenames, as the colons are incompatible with Singularity.
• Update task utils.rename_file to be more portable (was not working with miniwdl's implementation)
• In genbank_single, update more output filenames to be consistently named so we can more easily group them together.
• In task align_and_count, bugfix for empty input bams
• In task FastqToUBAM, add knobs for ram and disk size and increase defaults