Make outputs sync with metis model for bulk

[erflynn]

@AlaaALatif - thinking about this in response to the DL clean up, let's discuss

[erflynn]

discussed this during meeting on 12/8 -- Next steps:

• [ ] separated output into merged, and then per-sample output folders
• [ ] pull QC stats for each individual
• [ ] get rid of bams (b/c have crams and the bams are large)
• [ ] add merged_filtered vcf (see issue #52 post-merge filtering of variants in bulk pipeline)
• [ ] check with genomics whether there are additional items to add

@AlaaALatif @dtm2451

Example:

merged/
   mulitqc/
   results/ 
        merged_counts.tsv
        merged.vcf
        merged_filtered.vcf
    sample_sheet.csv
per-sample-outs/ 
   <Sample_id> /
       kallisto/
       qc/
       snps/
       star/