I realised that bowtie2 is picking up the bowtie directory. I have changed the PARAMS so this now selects the correct directory
I realised that bowtie2 is picking up the bowtie directory. I have changed the PARAMS so this now selects the correct directory

AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core