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Merge branch Issues#143 with master

Romain Therville requested to merge Issues#143_debug_init_illumina10X into 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))

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