some clean up

biopet/bamstats.wdl

biopet/biopet.wdl

build.sbt

bwa.wdl

common.wdl

cutadapt.wdl

fastqc.wdl

flash.wdl

gatk.wdl

gffcompare.wdl

gffread.wdl

hisat2.wdl

htseq.wdl

macs2.wdl

manta.wdl

mergecounts.wdl

multiqc.wdl

picard.wdl

project/build.properties

project/plugins.sbt