Add node filtering to samtools flagstat (#406932)
Rename bammarkduplicates output files (#406926)
Corrected filter flag from 0x9ff to 0x900
Rename markdup files
Merge remote-tracking branch 'js10-remote/devel' into devel

Conflicts:
	data/tophat2_sample_template.vtf
Merge remote-tracking branch 'wtsi-npg/devel' into devel