Bug fix: cutadapt report for paired-end read 1 and 2 were written to the same file
Added BQSR diagnostics (analyze covariates remaining after recalibration) according to GATK best practice docs
Changed rule for mergeing flowcell BAMs to sample BAMs in Makefile.halo, in order not to have unneccessary dependencies. As a result, it is no longer necessary to run "make -t samples" in HaloPlex workflow. Also changed some variable defs to use ":=" for increased speed.