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