Merge pull request #157 from dkj/devel2

check progress in staging by .bcl.gz files
Merge pull request #158 from wtsi-npg/devel

pull request from wtsi devel to master to create release 77.0
Merge pull request #159 from wtsi-npg/master

Merge pull request #158 from wtsi-npg/devel
Updates for handling references with transcriptome version
unused templates removed; samplesheets regenerated when the existing file is likely to originate  from an earlier or unknown run
Changes update; do not attempt to address a scenario with two pending runs for the same flowcell in the samplesheet daemon
modified so that a default transcriptome should not be used
ensure copyright belongs to GRL
Now using non-capturing group (?:) to simplying changes in reference::find . Extended reference-find test with transcriptome ref genome parsing
Merge branch 'devel' of https://github.com/wtsi-npg/npg_tracking into transcriptome
Changes file updated
Merge pull request #160 from mgcam/devel

samplesheet regenerated when the existing file does not come from the currently pending run
Merge remote-tracking branch 'jillian-remote/transcriptome' into devel2
Fix repository for transcriptome parse check