Merge branch Issues#143 with master

It's due to bug with the older version :

• just R1 and R2 files are used for analyses (ContaminationSearch, FastQC etc ... )
• R1, R2 and I1 after illuminaFilter if it's done are saved
• not impacted illlumina_qc analysis

Change :

• ng6_workflow
• add new function in utils for catch R1,R2 and I1 files after illuminafilter
• add new files to manage in smarty viszualisation

(Replaces the merge !68 (closed))