Merge branch 'develop' into fix-flexiprep

88776973 · Peter van 't Hof · ae622b72 · 1d3258b8 · 88776973 · 88776973
Commit 88776973 authored Oct 07, 2015 by Peter van 't Hof
--- a/public/biopet-extentsions/pom.xml
+++ b/public/biopet-extentsions/pom.xml
--- a/public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
+++ b/public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala