Clean folder

[thkuo]

• Where to put the smk scripts?
• Where to put the external scripts?
• Where to put the required software that are not available via conda?
• Working folder, results folder, and the program location
• Is there any software based on snakemake?

[thkuo]

Under the tmp folder, sub-folders are created by software (ie. bwa/stampy/vcftools...etc) instead of file types