Commits · 4557807c34834cdb35f54eaa3ca7e9d4f2ae10cb · Mirrors / biopet.biopet

25 Aug, 2014 3 commits

Peter van 't Hof authored Aug 25, 2014

Conflicts:
	flexiprep/nbactions.xml
	gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
	gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	mapping/examples/test.json
	mapping/nbactions.xml
	pom.xml

4557807c

Added BiopetPackage as complete package · 4f6ea975
Peter van 't Hof authored Aug 25, 2014

4f6ea975
Added single sample UnifiedGenotyper · 33b1e8fc
Peter van 't Hof authored Aug 25, 2014

33b1e8fc

22 Aug, 2014 6 commits
- Remove old functions · 4f24e9f3
  Peter van 't Hof authored Aug 22, 2014
  
  4f24e9f3
- convert AddOrReplaceReadGroups to biopet function · 3decab94
  Peter van 't Hof authored Aug 22, 2014
  
  3decab94
- convert MergeSamFiles to biopet function · dfed2154
  Peter van 't Hof authored Aug 22, 2014
  
  dfed2154
- Added skipMetrics option · 9b20e271
  Peter van 't Hof authored Aug 22, 2014
  
  9b20e271
- Added allSitePLs option · f6bbd1b0
  Peter van 't Hof authored Aug 22, 2014
  
  f6bbd1b0
- Convert SortSam to biopet function · f66115cc
  Peter van 't Hof authored Aug 22, 2014
  
  f66115cc
20 Aug, 2014 6 commits
- Merge origin/sander into peter · 2cd4fb00
  Peter van 't Hof authored Aug 20, 2014
  
  2cd4fb00
- Added BamOutput Option to Haplotypecaller · 8e97fe15
  Peter van 't Hof authored Aug 20, 2014
  
  8e97fe15
- Merge commit 'feeafebb ' into sander · 38acf7e0
  sajvanderzeeuw authored Aug 20, 2014
  
  38acf7e0
- Fix bug on single end library's · feeafebb
  Peter van 't Hof authored Aug 20, 2014
  
  feeafebb
- changed mem limit to 4gb · b68ea4a6
  sajvanderzeeuw authored Aug 20, 2014
  
  b68ea4a6
- Merge commit '18e080e1 ' into sander · 20871e07
  sajvanderzeeuw authored Aug 20, 2014
  
  20871e07
19 Aug, 2014 5 commits
- added all BWA options · d0768d9f
  sajvanderzeeuw authored Aug 19, 2014
  
  d0768d9f
- Moved Flexiprep val to root op mapping class · 18e080e1
  Peter van 't Hof authored Aug 19, 2014
  
  18e080e1
- Remove version command for picard · 89121481
  Peter van 't Hof authored Aug 19, 2014
  
  89121481
- Debug sickle wrapper · 7ab284fd
  sajvanderzeeuw authored Aug 19, 2014
  
  7ab284fd
- Fix bug when json parse failed · 3946dd26
  Peter van 't Hof authored Aug 19, 2014
  
  3946dd26
18 Aug, 2014 11 commits
- Fix bug on single end bam files · 22fdb87e
  Peter van 't Hof authored Aug 18, 2014
  
  22fdb87e
- Changed one option in BWA.scala so mapping had to be changed as well · 00b8265b
  sajvanderzeeuw authored Aug 18, 2014
  
  00b8265b
- Added all Sickle Options · f2db87ce
  sajvanderzeeuw authored Aug 18, 2014
  
  f2db87ce
- Added all BWA mem options · 4ddf34bf
  sajvanderzeeuw authored Aug 18, 2014
  
  4ddf34bf
- Change chunk directory · 1ca59443
  Peter van 't Hof authored Aug 18, 2014
  
  1ca59443
- Spelling fix · c36fb267
  Peter van 't Hof authored Aug 18, 2014
  
  c36fb267
- Changes actions for BedToIntervals tests · 3dbf492f
  Peter van 't Hof authored Aug 18, 2014
  
  3dbf492f
- Changed run to library · 7892b57c
  Peter van 't Hof authored Aug 18, 2014
  
  7892b57c
- Removed the Gatk-Old from the pom.xml · eac4ec9e
  Peter van 't Hof authored Aug 18, 2014
  
  eac4ec9e
- Changed Int to Long · 610b8971
  Peter van 't Hof authored Aug 18, 2014
  
  610b8971
- Fix bug on VariantEval -L option · 661c7456
  Peter van 't Hof authored Aug 18, 2014
  
  661c7456
15 Aug, 2014 2 commits
- Added a default vmem · 1f80f95b
  Peter van 't Hof authored Aug 15, 2014
  
  1f80f95b
- Skipping lines that are not correct bed entry's · a5876f3f
  Peter van 't Hof authored Aug 15, 2014
  
  a5876f3f
14 Aug, 2014 5 commits
- Added targetBed option · d8056e3d
  Peter van 't Hof authored Aug 14, 2014
  
  d8056e3d
- Added Vcf sample compare module · d94892dd
  Peter van 't Hof authored Aug 14, 2014
  
  d94892dd
- Added targetBait config option · 7729a31b
  Peter van 't Hof authored Aug 14, 2014
  
  7729a31b
- Fix array on json file · 0683782a
  Peter van 't Hof authored Aug 14, 2014
  
  0683782a
- Fix on end files on flexiprep, not intermediate anymore · 9d40cb55
  Peter van 't Hof authored Aug 14, 2014
  
  9d40cb55
12 Aug, 2014 2 commits
- Added md5sums for excutebles · de30ed59
  Peter van 't Hof authored Aug 12, 2014
  
  de30ed59
- Fix class name for report · 9ff06b99
  Peter van 't Hof authored Aug 12, 2014
  
  9ff06b99