[IlluminaWF] Change algo use with BWA for ContaminationSearch analysis

Currently, the ContaminationSearch analysis for illumina workflows is performed with bwa aln.
This algorithm is not optimal for the length of reads we currently have ; so we should use bwa mem.

Moreover, in the future pipeline under Nextflow we will use FastqScreen to make this analysis. This tool already use bwa mem.
So to have comparable results between the two pipelines, we must change bwa aln to bwa mem.