Mark DePristo f77d2e6965 Renamed NO_HEADER to the more accurate no_cmdline_in_header ... -- Also no_cmdline_in_header permits us to write contigs into the header, so that the shadow BCF system can work as well		2012-05-24 10:57:08 -04:00
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gatk	Renamed NO_HEADER to the more accurate no_cmdline_in_header	2012-05-24 10:57:08 -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