Commits · 05233c6bd5095fcc521750bc610e0b37de0eb6b2 · Mirrors / biopet.biopet

25 Nov, 2015 4 commits
- Move mini pipeline delly · 05233c6b
  Peter van 't Hof authored Nov 25, 2015
  
  05233c6b
- Merge branch 'feature-delly-merge' into shiva-refactor · 9c552b07
  Peter van 't Hof authored Nov 25, 2015
```
Conflicts:
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
```
  9c552b07
- Added CatVariants · 815a271f
  Peter van 't Hof authored Nov 25, 2015
  
  815a271f
- Remove whitespace · f64fad3c
  Peter van 't Hof authored Nov 25, 2015
  
  f64fad3c
24 Nov, 2015 9 commits
- Fixed outputDirs · 946ea4c2
  Peter van 't Hof authored Nov 24, 2015
  
  946ea4c2
- Convert breakdancer to sub pipeline of shiva · 60fc26c3
  Peter van 't Hof authored Nov 24, 2015
  
  60fc26c3
- Merge remote-tracking branch 'remotes/origin/develop' into feature-delly-merge · 2b63ae70
  Wai Yi Leung authored Nov 24, 2015
  
  2b63ae70
- Merge branch 'develop' into shiva-refactor · f85e71c2
  Peter van 't Hof authored Nov 24, 2015
  
  f85e71c2
- Merge branch 'release-0.5.0' into develop · abb2a281
  Peter van 't Hof authored Nov 24, 2015
  
  abb2a281
- Bump version to 0.6.0-SNAPSHOT · ac785920
  Peter van 't Hof authored Nov 24, 2015
  
  ac785920
- Bump version to 0.5.0 · c5303e8c
  Peter van 't Hof authored Nov 24, 2015
  
  c5303e8c
- Split into separated files · aefd3a63
  Peter van 't Hof authored Nov 24, 2015
  
  aefd3a63
- Split sv callers into separated classes · d97202a8
  Peter van 't Hof authored Nov 24, 2015
  
  d97202a8
23 Nov, 2015 9 commits
- Bump to 0.5.0-RC2 · 16d2711f
  Peter van 't Hof authored Nov 23, 2015
  
  16d2711f
- Added summary jobs to toucan · 5f03d3de
  Peter van 't Hof authored Nov 23, 2015
  
  5f03d3de
- Added target variants to report · 6f6a76e7
  Peter van 't Hof authored Nov 23, 2015
  
  6f6a76e7
- Added intermediate · 27813378
  Peter van 't Hof authored Nov 23, 2015
  
  27813378
- Fixed nameprefix · 38402a6c
  Peter van 't Hof authored Nov 23, 2015
  
  38402a6c
- Added tbi output file · ba626927
  Peter van 't Hof authored Nov 23, 2015
  
  ba626927
- Added module to config value · 2c8b6f02
  Peter van 't Hof authored Nov 23, 2015
  
  2c8b6f02
- Adding decompose option to shiva · 04f343cb
  Peter van 't Hof authored Nov 23, 2015
  
  04f343cb
- Adding vt decompose extension · cf338a86
  Peter van 't Hof authored Nov 23, 2015
  
  cf338a86
20 Nov, 2015 7 commits
- Added normalize option to shiva · ac9315e7
  Peter van 't Hof authored Nov 20, 2015
  
  ac9315e7
- Fixed args · 73088af2
  Peter van 't Hof authored Nov 20, 2015
  
  73088af2
- Added vt normalizer extension · 241a7d23
  Peter van 't Hof authored Nov 20, 2015
  
  241a7d23
- Fixed summary jobs for carp · 1568a600
  Peter van 't Hof authored Nov 20, 2015
  
  1568a600
- Added vcf stats for each region bed file · 991c07af
  Peter van 't Hof authored Nov 20, 2015
  
  991c07af
- Remove addSummaryJobs() · ea781d9b
  Peter van 't Hof authored Nov 20, 2015
  
  ea781d9b
- Split variantcalllers in separated files · 89b7a259
  Peter van 't Hof authored Nov 20, 2015
  
  89b7a259
19 Nov, 2015 8 commits
- Fixed bowtie index · 7a8ef0e4
  Peter van 't Hof authored Nov 19, 2015
  
  7a8ef0e4
- Bumb version to 0.5.0-RC1 · 19a93bbb
  Peter van 't Hof authored Nov 19, 2015
  
  19a93bbb
- Fixed license headers · fceb39a9
  Peter van 't Hof authored Nov 19, 2015
  
  fceb39a9
- Fixed License files · d5fbab5b
  Peter van 't Hof authored Nov 19, 2015
  
  d5fbab5b
- Sync with develop · 38461999
  Wai Yi Leung authored Nov 19, 2015
  
  38461999
- Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-delly-merge · 8c50da88
  Wai Yi Leung authored Nov 19, 2015
  
  8c50da88
- Merge branch 'fix-tools_mainclass' into 'develop' · bd7ca140
  Sander Bollen authored Nov 19, 2015
```
Fixed bug in loading the mainClass for biopet tools

Fixes a small bug in loading the mainClass of tools.

When jenkins don't complain this can be merged.

See merge request !281
```
  bd7ca140
- Fixed bug in loading the mainClass for biopet tools · 7f424eb9
  Peter van 't Hof authored Nov 19, 2015
  
  7f424eb9
18 Nov, 2015 3 commits
- Merge branch 'feature-docs-0.5_quickfix' into 'develop' · 74f301a6
  Peter van 't Hof authored Nov 18, 2015
```
Error in Gentrap sample config in Documentation

Please collect all minor documentation things in this ticket.

See merge request !280
```
  74f301a6
- Merge branch 'feature-core_testing' into 'develop' · f55fdeda
  Sander Bollen authored Nov 18, 2015
```
Added unit tests

see also #51 

See merge request !278
```
  f55fdeda
- Merge branch 'fix-toucan' into 'develop' · b5500137
  Sander Bollen authored Nov 18, 2015
```
Fix toucan



See merge request !279
```
  b5500137