Add globals option to sample input YAML files. Enables specification of shared files a single time making avoiding copy paste and making updates available. Automatically create globals in template functionality if present
Integrate validation plots into standard workflow. Currently requires manually installation of prettyplotlib into bcbio python site-packages until next release
Fixes global options being looked up by value instead of key.
Remove debugger usage.
Fixes: revert 457cd7641a with better documentation and checking for non-hashable values; sorry @roryk for the issue. Correctly ensure all samples are passed back from validation.
Ensure finding of cutadapt installed in local Anaconda python directory. Fixes #295
Ensure track and browser lines are removed from input BED file before feeding to SnpEff #216