genbank prep and assemble_denovo updates #443
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…out_prefix happens to be an accession; also prevent combined fasta from showing up in genomes_fasta
…enable to accepting the output of scaffolding_chosen_ref as input
…rite bam headers and fasta headers
dpark01
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genbank: dust off genbank prep workflow, update it to make it more smooth to run after a series of assemble_denovo or assemble_refbased runs in Terra, have it figure out more things by itself, add hard assumption that annotations will be transferred from a genbank genome. Fix annotation transfer for sequences with filename-unfriendly names.assemble_denovo: slight tweaks to denovo assembly workflow inputs/outputs/cleanups, allow it to parallelize across and merge results from multiple input bams, emit assembly_method by default