I have modified the Bowtie mapper class because the index for bowtie2 was not being set and was picking up the bowtie index dir
I have modified the Bowtie mapper class because the index for bowtie2 was not being set and was picking up the bowtie index dir

CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines