Quality of life improvements

[AroneyS]

Handle env variables better

• Rename aviary-gtdbtk-dir and aviary-checkm2-dir to *-db
• Add database env variables to ibis build (SingleM, CheckM2, GTDBtk)
• Delete build folder on build start
• Ibis build example indicate that argument is for conda env folder
• Add TMPDIR env variable to ibis build (defaults to /tmp)
• Pass TMPDIR env variable to Aviary
• Add aviary build to ibis build? - --skip-long-reads
• Load from env variables if arg not provided
• Pass conda env path to Aviary

No genomes updates

• Add --no-genomes to ibis update
• Add schema to no_genomes.py csv loading
• Notify if any samples from pipe are empty?

Minimise standard workflow arguments

• Load samples and genomes from config if not provided to ibis iterate
• Check standard aviary output location if aviary outputs and new genomes not provided to ibis iterate
• Create cumulative skip_coassemblies input that is loaded by iterate
• Check standard sample SingleM dir if not provided to ibis iterate
• Check standard read_size file if not provided to ibis iterate
• Remove --no-genomes argument and set if arg not provided
• Update warning ibis.py line 763
• Update iterate examples in help and README
• Set max size to 50Gbp unless single-assembly

Bump major version due to breaking changes

• --coassemble-output now refers to --output dir from coassemble command instead of referring to the coassemble subfolder within that output dir
• Removed --no-genomes argument and made that the default
• Rename --aviary-[gtdbtk, checkm2]-dir args to --aviary-[gtdbtk, checkm2]-db