Guillermo del Angel c9d3c67a9b Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity: ... -- Picard extension so Queue scripts can use FastqToSam -- Single-sample BAM processing: merge/trim reads + BWA + IR + MD + BQSR. Mostly identical to standard pipeline, except for the adaptor trimming/merging which is critical for short-insert libraries. -- Single-sample calling (experimental, work in progress): standard UG run but outputting at all sites, meant for deep whole genomes. New scripts		2013-04-08 11:52:13 -04:00
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engine	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
extensions	Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity:	2013-04-08 11:52:13 -04:00
function	Added a QFunction.jobLocalDir for optionally tracking a node local directory that may have faster intermediate storage, with SGF ensuring that if the directory happens to be on the same machine that it get's a clone specific sub-directory to avoid collisions.	2013-01-25 14:28:04 -05:00
library	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
util	Re-committing the following changes from Dec 18:	2013-01-16 12:43:15 -05:00
QCommandLine.scala	Message "script failed" moved to the correct place in the code	2013-02-04 15:37:23 -05:00
QCommandPlugin.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QException.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QScript.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QScriptManager.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QSettings.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00