SUPER v4.0
Adapt script for all users and:
- New Commands.log in each run
- Change method to introduce files to analyse (--path is changed by --input). Input could be a file with all files, a list, or the path.
- Change --bwa_dir by --out_dir, with an absolut/relative path for all Super results
- Add samtools mpileup "-C 50" option
- Add Gatk tools for Indels
- Add --treat_bam option to clean bam files for analysing