added YeowareUtils.scala that replaces /projects/ps-yeolab and /home/gpratt with environment var $GENOME
Merge branch 'master' of https://github.com/mlovci/gatk
fixed bugs in yeowareutils scala file
Merge branch 'master' of https://github.com/mlovci/gatk
i hate scala
Merge branch 'master' of https://github.com/mlovci/gatk
change default fastqc location... so fastqcs won't go to the source folder
added (unused) @Input indexFile input for Miso so it waits for bam indexing to finish
Merge branch 'master' of https://github.com/mlovci/gatk
named miso runner better, changed output to a file that isn't an intermediate and set nCoresRequest == 16
update miso parameter
declaring variables is dumb
fixed conflict in miso file
fixed errors in miso
Merge pull request #6 from mlovci/master

added yeowareutils