Merge branch 'master' of github.com:allPowerde/ngsane
RNA-SeqQC is now running on CSIRO
Bugfix tophatcuff was still commented out
typo removed and example provided
wiggler mod added

work in progress
fastxtrimming replaced by trimmomatic
trimmomatic mod added
wiggler mod added
Default thread parameters adjusted
tmp files removed
restriction enzyme specified in genomedb
Remove sam files immediately after bam conversion
Changes to --library type ht-seq-count and BamToWw

-- added support for fr-second strand
-- added -f 3 flag to take properly paired reads in ht-seq-count inputs
-- added ht-seq-count  --strict and --non empty intersection types to
genegcode gene level summaries
-- commented out ht-seq-count transcripts for the moment while
prototyping.
-- added samtools view -f3 tagged bam to tophat out dir.
convert bowtie output to bam straight away
favor bam generation in mapping piplines
switch default mapping to bwa
revert RNAseq-QC handling
use BWA as default
adjust default wiggler resources
tophat options provided in sample config