Commits · 30696cabc25d1250de1e07b11bef6a8c24c78510 · Mirrors / biopet.biopet

Jan 19, 2016
- Fixed unit tests · 30696cab
  Peter van 't Hof authored 9 years ago
  
  30696cab
- Added varscan_jar to test config · dd9a7060
  Peter van 't Hof authored 9 years ago
  
  dd9a7060
- Raise default memory for varscan · 10835803
  Peter van 't Hof authored 9 years ago
  
  10835803
- Added version to varscan · 3f85a446
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit a13b0d1d)
  3f85a446
- Fixed style · 8b099b94
  Peter van 't Hof authored 9 years ago
  
  8b099b94
- add varscan test to shiva variantcalling test · 86ad2593
  Sander van der Zeeuw authored 9 years ago
  
  86ad2593
- move varscan wrapper to extensions · ca40d875
  Sander van der Zeeuw authored 9 years ago
  
  ca40d875
Jan 18, 2016
- changes to get rid of reference calls · bb46c239
  Sander van der Zeeuw authored 9 years ago
  
  bb46c239
- delete file name file on exit of pipeline · 59923a55
  Sander van der Zeeuw authored 9 years ago
  
  59923a55
- change sample name in varscan vcf · 64325f97
  Sander van der Zeeuw authored 9 years ago
  
  64325f97
- remove function removeEmptyPile() · a35c3c9c
  Sander van der Zeeuw authored 9 years ago
  
  a35c3c9c
- added fix mpileup.py scripts to scripts dir in shiva · 7a5e1b5c
  Sander van der Zeeuw authored 9 years ago
  
  7a5e1b5c
- added fixmpileup script and removeEmptypile function · 328be9a6
  Sander van der Zeeuw authored 9 years ago
  
  328be9a6
Jan 15, 2016
- bgzip piping went wrong fix with if stdout else > · 43748908
  Sander van der Zeeuw authored 9 years ago
  
  43748908
- generate dir for varscan · c22edcf3
  Sander van der Zeeuw authored 9 years ago
  
  c22edcf3
- add varscan to shiva variantcallers · 559881ed
  Sander van der Zeeuw authored 9 years ago
  
  559881ed
Jan 14, 2016

Merge branch 'feature-gentrap_report' into 'develop' · 9e62862f

Wai Yi Leung authored 9 years ago

Feature basic gentrap report

Part of #223 

This only contains basic stats, no gentrap specific stats added.

See merge request !302

9e62862f

Jan 12, 2016
- Merge branch 'fix-spelling-errors_2016-jan' into 'develop' · c03da5b9
  Peter van 't Hof authored 9 years ago
  
  Fix spelling error in the WriteDependencies JSON output Fix the output keys for the JSON output of `writedependencies`. See merge request !305
  c03da5b9
- Fix spelling error in the WriteDependencies JSON output · bfc93ed3
  Wai Yi Leung authored 9 years ago
  
  bfc93ed3
- Style fixes · 9968c43a
  Peter van 't Hof authored 9 years ago
  
  9968c43a
- Added more fields · 012fc811
  Peter van 't Hof authored 9 years ago
  
  012fc811
- Fix metrics · b93f2642
  Peter van 't Hof authored 9 years ago
  
  b93f2642
- Merge branch 'fix-toucan' into 'develop' · edbabec1
  Wai Yi Leung authored 9 years ago
  
  Fix short name See merge request !303
  edbabec1
- Fix short name · d46354a7
  Peter van 't Hof authored 9 years ago
  
  d46354a7
- Added rna · ae1b86f2
  Peter van 't Hof authored 9 years ago
  
  ae1b86f2
- Fix labels · 19a8e5d7
  Peter van 't Hof authored 9 years ago
  
  19a8e5d7
- Added rna metrics plot · dd6189e2
  Peter van 't Hof authored 9 years ago
  
  dd6189e2
- Only show wgs if executed · b9f23956
  Peter van 't Hof authored 9 years ago
  
  b9f23956
- Fix reference tag · 81d36084
  Peter van 't Hof authored 9 years ago
  
  81d36084
- Added html report to pipeline · 189a25d4
  Peter van 't Hof authored 9 years ago
  
  189a25d4
- Merge remote-tracking branch 'remotes/origin/develop' into feature-gentrap_report · 759b7f36
  Peter van 't Hof authored 9 years ago
  
  759b7f36
- Merge branch 'feature-gentrap_to_multisamplemapping' into 'develop' · e2126bad
  Wai Yi Leung authored 9 years ago
  
  Switch gentrap to multisample mapping Fixes #256 See merge request !299
  e2126bad
- Fixed report types · 9034e179
  Peter van 't Hof authored 9 years ago
  
  9034e179
Jan 11, 2016
- Change gentrap report to multisample mapping report · 56766d98
  Peter van 't Hof authored 9 years ago
  
  56766d98
- Added front · be731b74
  Peter van 't Hof authored 9 years ago
  
  be731b74
- Switch shiva to general multisample report · b0f9d027
  Peter van 't Hof authored 9 years ago
  
  b0f9d027
- Remove outdated todo · d79733d1
  Peter van 't Hof authored 9 years ago
  
  d79733d1
- Added report to multisample mapping · b44d0a54
  Peter van 't Hof authored 9 years ago
  
  b44d0a54
- Move generic pages to multisamplemapping · aa8071f2
  Peter van 't Hof authored 9 years ago
  
  aa8071f2
- Merge branch 'feature-varda' into 'develop' · 3a13df98
  Peter van 't Hof authored 9 years ago
  
  Feature varda fixes #208 This is to track this branch in jenkins See merge request !245
  3a13df98