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need GenePattern modules for the latest Picard tools
(repost of part of a mail to Picard team)
Is there someone out there having new GP modules for as many as possible Picard.jar subcommands (I love them all)
I am preparing a variant training for the fall on our institute in-dev-Genepattern server and would love to teach people use the new Picard as often as possible (and when it opens, will also love to add GATK v4).
The problem for Picard tools is that the java command has changed from a ‘command.jar’ to a ’picard.jar subcommand’ and some arguments may have been added or modified which makes the process of old GP module recycling useless.
The good news is that the new core argument syntax has been made uniform, it may therefore be better to start from scratch and create a generic GP module that fits them (almost) all??
If someone could provide such basic module (or more :-), it would be greatly appreciated.