Commits · 56e6f732ed12d41f1c2919de0479e2153086d7a0 · Mirrors / biopet.biopet

19 Jan, 2016 3 commits
- Integrating develop · 56e6f732
  Wai Yi Leung authored Jan 19, 2016
  
  56e6f732
- Merge branch 'feature-update-cutadapt' into 'develop' · ac55539b
  Peter van 't Hof authored Jan 19, 2016
```
Update Cutadapt wrapper

Updated cutadapt wrapper to reflect cutadapt 1.9 and added missing options (which were already supported in 1.5 but not in extension)

Closes #243 

See merge request !310
```
  ac55539b
- Update Cutadapt wrapper and style change (camelCaps instead of _) · 3049d572
  Wai Yi Leung authored Jan 19, 2016
  
  3049d572
18 Jan, 2016 1 commit
- Update Cutadapt wrapper · 564081d7
  Wai Yi Leung authored Jan 18, 2016
  
  564081d7
17 Jan, 2016 2 commits
- Merge branch 'feature-core_unit_tests' into 'develop' · defe2788
  Wai Yi Leung authored Jan 17, 2016
```
Feature core unit tests

Fixes #253 

See merge request !307
```
  defe2788
- Merge branch 'fix-renames' into 'develop' · acf6fe14
  Peter van 't Hof authored Jan 17, 2016
```
Fix renames

Some naming fixes for consistency.

See merge request !309
```
  acf6fe14
15 Jan, 2016 5 commits
- Rename camel caps to underscore · 793a34eb
  bow authored Jan 15, 2016
  
  793a34eb
- Unify output bam names · a3009b39
  bow authored Jan 15, 2016
  
  a3009b39
- Added test to summary core · 6e26a6ec
  Peter van 't Hof authored Jan 15, 2016
  
  6e26a6ec
- Adding empty summary test · 6f7fe187
  Peter van 't Hof authored Jan 15, 2016
  
  6f7fe187
- Optimize imports · 58369dd0
  Peter van 't Hof authored Jan 15, 2016
  
  58369dd0
14 Jan, 2016 6 commits
- Adding tests for input files for summary · 684fe7c8
  Peter van 't Hof authored Jan 14, 2016
  
  684fe7c8
- Add test addSummarizable · 645895a0
  Peter van 't Hof authored Jan 14, 2016
  
  645895a0
- Added simple test for summaryQscript · 5fe478bc
  Peter van 't Hof authored Jan 14, 2016
  
  5fe478bc
- Added test for summarizable · acbf24e0
  Peter van 't Hof authored Jan 14, 2016
  
  acbf24e0
- Fixed reference test · be4fc224
  Peter van 't Hof authored Jan 14, 2016
  
  be4fc224
- Merge branch 'feature-gentrap_report' into 'develop' · 9e62862f
  Wai Yi Leung authored Jan 14, 2016
```
Feature basic gentrap report

Part of #223 

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

See merge request !302
```
  9e62862f
12 Jan, 2016 16 commits
- Merge branch 'fix-spelling-errors_2016-jan' into 'develop' · c03da5b9
  Peter van 't Hof authored Jan 12, 2016
```
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 Jan 12, 2016
  
  bfc93ed3
- Style fixes · 9968c43a
  Peter van 't Hof authored Jan 12, 2016
  
  9968c43a
- Added more fields · 012fc811
  Peter van 't Hof authored Jan 12, 2016
  
  012fc811
- Fix metrics · b93f2642
  Peter van 't Hof authored Jan 12, 2016
  
  b93f2642
- Merge branch 'fix-toucan' into 'develop' · edbabec1
  Wai Yi Leung authored Jan 12, 2016
```
Fix short name



See merge request !303
```
  edbabec1
- Fix short name · d46354a7
  Peter van 't Hof authored Jan 12, 2016
  
  d46354a7
- Added rna · ae1b86f2
  Peter van 't Hof authored Jan 12, 2016
  
  ae1b86f2
- Fix labels · 19a8e5d7
  Peter van 't Hof authored Jan 12, 2016
  
  19a8e5d7
- Added rna metrics plot · dd6189e2
  Peter van 't Hof authored Jan 12, 2016
  
  dd6189e2
- Only show wgs if executed · b9f23956
  Peter van 't Hof authored Jan 12, 2016
  
  b9f23956
- Fix reference tag · 81d36084
  Peter van 't Hof authored Jan 12, 2016
  
  81d36084
- Added html report to pipeline · 189a25d4
  Peter van 't Hof authored Jan 12, 2016
  
  189a25d4
- Merge remote-tracking branch 'remotes/origin/develop' into feature-gentrap_report · 759b7f36
  Peter van 't Hof authored Jan 12, 2016
  
  759b7f36
- Merge branch 'feature-gentrap_to_multisamplemapping' into 'develop' · e2126bad
  Wai Yi Leung authored Jan 12, 2016
```
Switch gentrap to multisample mapping

Fixes #256 

See merge request !299
```
  e2126bad
- Fixed report types · 9034e179
  Peter van 't Hof authored Jan 12, 2016
  
  9034e179
11 Jan, 2016 7 commits
- Change gentrap report to multisample mapping report · 56766d98
  Peter van 't Hof authored Jan 11, 2016
  
  56766d98
- Added front · be731b74
  Peter van 't Hof authored Jan 11, 2016
  
  be731b74
- Switch shiva to general multisample report · b0f9d027
  Peter van 't Hof authored Jan 11, 2016
  
  b0f9d027
- Remove outdated todo · d79733d1
  Peter van 't Hof authored Jan 11, 2016
  
  d79733d1
- Added report to multisample mapping · b44d0a54
  Peter van 't Hof authored Jan 11, 2016
  
  b44d0a54
- Move generic pages to multisamplemapping · aa8071f2
  Peter van 't Hof authored Jan 11, 2016
  
  aa8071f2
- Merge branch 'feature-varda' into 'develop' · 3a13df98
  Peter van 't Hof authored Jan 11, 2016
```
Feature varda

fixes #208 

This is to track this branch in jenkins

See merge request !245
```
  3a13df98