suppress message from existing dirs when running mkdir
suppress number of non-important error messages
Bowtie module replaced
merged with upstream master
Tophay and Cufflinks included
Merge remote-tracking branch 'upstream/master'
#52 Java warning fixed
#52 Bugfix for bowtie and tophad
Bugfix test for mget functionality
#54 bugfix bowtie run on input with non fasta file suffixes
#55 trim galore module added
#56 hicup module added
#57 zip trimmed fastq files
use pigz for parallel zipping if available
hiclib addition to ngsane (wip)
specific additions for the local SGE cluster
hiclib trigger script added (wip)
Bugfix list of tasks revived
HICLIB variables adjusted
Merge branch 'master' of github.com:Gurado/ngsane