Merge pull request #483 from CCBR/activeDev

merging 4.0.6 into master

Adding JDK inflater/deflater options to BaseRecalibrator for AMD nodes

moving tag

Tagging activeDev version with ChIP-seq patches

version 4.0.3

removed AVIA

Merging activeDev for v4.0.1 release (#444)

* Fix sequenza error

* Scrnaseq (#437)

Scrnaseq: miRNA-seq changes and scRNA-seq changes

* Symlink counts matrix if "counts/" exists in users rawdata directory

* Dectect if users is starting from a raw counts matrix

* Updating pop-up box dialogue after detection of new counts matrix filetype

* Find differential expression metadata in "/path/to/rawdata/counts/"

* Readability: checking for counts matrix outside conditional statement

* Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR

* Explicitly loading 'python/2.7': default version of python changing to '3.7'

Co-authored-by: Mayank  Tandon <[email protected]>
Co-authored-by: wong-nw <[email protected]>
Co-authored-by: jlac <[email protected]>

Tagging activeDev with "v4.0.0"

synced activeDev with CCBR_Pipeliner_3.0

ChIP-seq bug fix and gui additions