save seqchksum files
use samtools merge instead of bamcat because of deadlock problems
some changes to parmater names to follow new input/output convention
alignment_wtsi_stage2_template.json
  added outputs for new samtools stats reports

final_output_prep.json
  added -F 0x900 filter flag to bamcheck
  added outputs for new samtools stats reports
  added samtools_executable param to allow selection of samtools version

post_alignment.json
  added samtools_executable param to allow selection of samtools version

seqchksum.json
  changed from bamcat to samtools merge to avoid deadlock
  added samtools_executable param to allow selection of samtools version