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4 Commits (a10b2a00a55ec85d3d4d64249aed060abb9367d4)

Author SHA1 Message Date
kshakir fd5970fdd4 At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them. 
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 21:30:48 +00:00
kshakir 3aedd0055e Updated firehose clean bam pipeline to pull firehose info and push back firehose clean bam. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4088 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 20:38:42 +00:00
kshakir 618c69f8dc More updates to the CleanBamFile pipeline. 
Added the a CommandLineFunction.jobDependencies that will explicitly force a function to wait for a file, even if the value isn't otherwise listed on an @Input.
More bug fixes and refactoring of functions.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4048 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-17 14:59:42 +00:00
kshakir 307c8ca027 Created a new playground script for cleaning bams in Firehose. 
Some refactoring of Queue extensions for reusability in scripts.
Putting the extensions into the Queue.jar after building them.
More updates to GATK walker arguments specifying @Input and @Output for Queue.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4032 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-13 23:52:24 +00:00