Khalid Shakir 91cb654791 AggregateMetrics: ... - By porting from jython to java now accessible to Queue via automatic extension generation. - Better handling for problematic sample names by using PicardAggregationUtils. GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name. CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering. Added SelectHeaders walker for filtering headers for dbGAP submission. Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter. Latest WholeGenomePipeline. Other minor cleanup to utility methods.		2012-04-17 11:45:32 -04:00
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gatk	AggregateMetrics:	2012-04-17 11:45:32 -04:00
picard	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
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