Devel - Githubissues

b97pla commented 8 years ago

This is a PR to merge the latest developments into master. Changes include:

If given a GATK stand-alone license on the command line, the phone home feature of GATK will be disabled
Introduced a command-line argument to set how qualimap will treat duplicate reads. Default is to use the duplicates marked by picard.
Improved build process to include the option to create deployable zip-files
Removed bundling of sbt version, which means tests depending on the testNG have been disabled.

When merged, this should probably be tagged as a new release.

b97pla commented 8 years ago

:hand: Wait with merging this PR until we are sure we've included everything needed for setting up Piper with the module system.

b97pla commented 8 years ago

@johandahlberg do you think this can be merged now?

NationalGenomicsInfrastructure / piper