Isoform quantification & restructuring

[acesnik]

• Removed aspera-cli because SRA-prefetch isn't really using it but still getting 10x faster downloads with HTTPS than fasterq-dump
• Adding quick quantification with StringTie2 of both assembled isoforms and reference transcripts, and summarizing the quant results in a table
• Removing fusion workflow, since it's not integrated and I don't have plans to do so in the near future
• Removed duplicate biopython reference
• Restructuring folders according to https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html
• Using conda environments for every rule to allow snakemake --use-conda to be more efficient if a subset of workflows is selected
• Removed -SO coordinate from AddReadGroups in variant workflow because it looks like that triggers a followup sort
• Allocated double GATK's normal RAM to MarkDuplicates because it runs close to the RAM limit