v6.0.0

What's Changed

*Perform submission in batches using batch_size param
*Run a submission dry run using dry_run param (creates a submission.log file in the submission outdir)
*Use true, unmodified nf-core versions of nf-core bakta modules
*Add a registry param for quay.io, and modify dockerhub container prefixes to accommodate
*Change output_dir to outdir everywhere
*Integrate "nanopore, illumina, or illumina & nanopore" for SRA submissions
*Fixes a lot of dperecated/incorrect Nextflow syntax stuff
*Incorporates basic nf-tests for all modules and subworkflows (full pipeline nf-test coming in a future update)
*Includes re-writes and/or restructuring of most workflows/subworkflows
*For AWS -> will fetch the files from AWS, download to local, then upload to ftp (cloud-to-cloud coming in a future update)
*Probably a lot of other stuff I'm forgetting...
@jessicarowell in #323

Full Changelog: v5.2.6...v6.0.0