Changed all "mbuffer" and "tee" commands to "teepot" commands
amended some "ioport" names to match preferred naming convention (name should include "IN" or "OUT")
tee exec node fixes following change from mbuffer to teepot
Remove hardcoded paths
Merge pull request #4 from dkj/devel

teepot tweaks
small fix to output file name in examples
added subst_param_name "phix_or_target" to md5 file name produced by bamrecompress
added subst_param_name "phix_or_target" to index file name produced by bamrecompress, and
to calibration_pu
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
removed unused edges
dealt with warnings of udefined variables
simplified some logging messages which were using out-of-date attributes
large wait (500 minutes) to avoid unnecessary spill to disk

had previously been an mbuffer
Merge pull request #5 from dkj/devel

large wait (500 minutes) to avoid unnecessary spill to disk
Merge pull request #54 from dozy/mbuffer_to_teepot

convert mbuffer and tee to teepot