lofreq task portability, misc other edits

[dpark01]

This PR introduces 3 small unrelated improvements:

1. task lofreq was written in a way that presumed writability of new files in the localization directory. This fails in execution environments that mount input files into the container as read only. Change WDL task behavior to make local copies before indexing.
2. Rename WDL task ncbi.package_genbank_ftp_submission to ncbi.package_sc2_genbank_ftp_submission, since the format of the zip package produced is not universally accepted for all species at Genbank yet.
3. assemble_denovo: percolate sample_name to scaffolding input so that output fasta files are named properly.