Guillermo del Angel 5fac5bf12e Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars. ... > Also, reenable joint cleaning as now it works. > DEV-125 #resolve > DEV-90 #resolve		2012-10-23 14:08:31 -04:00
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cancer	upgraded mutation caller with VCF output	2012-10-15 13:49:08 -04:00
gatk	When gathering VCFs, using CombineVariants from the current classpath, and not the GATK used to run the command. This was a concern for external modules that bundled the engine but not CombineVariants.	2012-10-23 12:44:06 -04:00
picard	Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars.	2012-10-23 14:08:31 -04:00
samtools	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
snpeff	Be explicit about setting the snpEff -onlyCoding option in the pipeline	2012-01-17 20:04:27 -05:00