convex_plots step and test should not work
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
add convex_mean_mad step; and adjust many of the convex related steps; temporarily broken pipeline
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
overhaul of convex pipelines to get better workflow

convex pipeline chain can now be set up at the start witout having to wait for each pipeline to finish in turn
Merge branch 'release/0.195' into develop
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/convex_mad
update test vep_cache for v75; fix link for v73
Merge branch 'feature/convex_rearrange' into develop
fix verify bam id step and pipeline

- vcf should be an input option, not metadata in the input bam file
- include freemix and other metrics as metdata so can be used in future auto qc steps
Merge branch 'feature/verifybamid_fix' into develop
new STAR rna-seq realignment pipeline
improvements to star pipeline and test suite
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
version bump