Fixed 2 bugs in bowtie2.cfmod bowtie2 path selection
Bug 1: bowtie2 path was never accepted unless bowtie1 path existed
Bug 2: bowtie2 path was never replaced with bowtie1 path in the case where bowtie1 path exists but bowtie2 path doesn’t
Give more info to cfmods to decide memory and cores requirements.

In cf, decide cores and memory only after determining prev_job etc. More parameters now fed to —-mem and —-cores decision process so that more memory can be requested for bigger files and can be controlled in pipeline file.
e.g. in .cfmod, to pass h_vmem request from pipeline arg “h_vmem”:
if($required_mem){
	my @h_vmem = ("");
	my ($files, $runfile, $job_id, $prev_job_id, $cores, $mem, $parameters, $config_ref) = CF::Helpers::load_runfile_params(@ARGV);
	@h_vmem = grep(/^h_vmem$/, @$parameters);
	print $h_vmem[0].CF::Helpers::allocate_memory($required_mem, '8G', ‘80G');
	exit;
}