Commits · 9620a19a06801515e0db282e2fa9fc150e875297 · Mirrors / biopet.biopet

26 Jul, 2017 6 commits
- Fixed typo that caused compile error · 9620a19a
  Ruben Vorderman authored Jul 26, 2017
  
  9620a19a
- Edited gearsreport · e937a04d
  Ruben Vorderman authored Jul 26, 2017
  
  e937a04d
- Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-669 · 0a28700b
  Ruben Vorderman authored Jul 26, 2017
```
# Conflicts:
#	biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
#	flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
#	flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
#	gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
```
  0a28700b
- Gearsreport completely defutured · 763f8f4d
  Ruben Vorderman authored Jul 26, 2017
  
  763f8f4d
- defutured flexiprepBaseSummary.ssp · 97661f8f
  Ruben Vorderman authored Jul 26, 2017
  
  97661f8f
- readsummaryplot defutured. New summaryPlotLines function added. · dd62378d
  Ruben Vorderman authored Jul 26, 2017
  
  dd62378d
25 Jul, 2017 15 commits
- Merge pull request #167 from biopet/fix-BIOPET-755 · df582f1a
  Peter van 't Hof authored Jul 25, 2017
```
Small fixes for Gentrap
```
  df582f1a
- Merge pull request #166 from biopet/fix-BIOPET-718 · 23bdc5b2
  Peter van 't Hof authored Jul 25, 2017
```
Removing sample/library variantcalling
```
  23bdc5b2
- Adding more default memory · 931771fe
  Peter van 't Hof authored Jul 25, 2017
  
  931771fe
- No merging with only 1 sample · 23a0b18f
  Peter van 't Hof authored Jul 25, 2017
  
  23a0b18f
- Adding default gtf file to STAR · 532f837c
  Peter van 't Hof authored Jul 25, 2017
  
  532f837c
- Start on defuturing readsummaryplot · 4e394bc9
  Ruben Vorderman authored Jul 25, 2017
  
  4e394bc9
- Fixing arguments · 250e63be
  Peter van 't Hof authored Jul 25, 2017
  
  250e63be
- Simplified structure · 83188c3f
  Ruben Vorderman authored Jul 25, 2017
  
  83188c3f
- Style changes · f3071de2
  Peter van 't Hof authored Jul 25, 2017
  
  f3071de2
- Fixing tests · 565cb85a
  Peter van 't Hof authored Jul 25, 2017
  
  565cb85a
- FlexiprepReadSummary.ssp defutured · 8263ea12
  Ruben Vorderman authored Jul 25, 2017
  
  8263ea12
- FlexiprepReadSummary.ssp defutured · 03fa2c53
  Ruben Vorderman authored Jul 25, 2017
  
  03fa2c53
- Removing sample and library variantcalling · c46b3983
  Peter van 't Hof authored Jul 25, 2017
  
  c46b3983
- Completed sortableThemeBootstrap dictionary. · 36b45eb4
  Ruben Vorderman authored Jul 25, 2017
  
  36b45eb4
- Merge pull request #165 from biopet/fix-BIOPET-750 · c913b602
  Peter van 't Hof authored Jul 25, 2017
```
Adding spark support for VcfStats
```
  c913b602
24 Jul, 2017 15 commits
- Merge pull request #164 from biopet/fix-BIOPET-752 · dc145917
  Peter van 't Hof authored Jul 24, 2017
```
Adding option to also run qiime with multiple samples at once
```
  dc145917
- Merge pull request #163 from biopet/fix-BIOPET-753 · 1e8b3c2f
  Peter van 't Hof authored Jul 24, 2017
```
Fixing summary in Basty
```
  1e8b3c2f
- Skipping double checkChecksum jobs · 6bda10a5
  Peter van 't Hof authored Jul 24, 2017
  
  6bda10a5
- Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-753 · 03beb3f1
  Peter van 't Hof authored Jul 24, 2017
  
  03beb3f1
- Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-750 · db65e3d7
  Peter van 't Hof authored Jul 24, 2017
```
# Conflicts:
#	biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
```
  db65e3d7
- Merge remote-tracking branch 'remotes/origin/fix-BIOPET-750' into fix-BIOPET-750 · 5c5ae1cd
  Peter van 't Hof authored Jul 24, 2017
  
  5c5ae1cd
- Merge pull request #162 from biopet/fix-BIOPET-745 · 5d3b5448
  Peter van 't Hof authored Jul 24, 2017
```
Fixing some failing tests
```
  5d3b5448
- Merge pull request #148 from biopet/fix-BIOPET-732 · d452d397
  Peter van 't Hof authored Jul 24, 2017
```
Fix fastq sync prefixes
```
  d452d397
- started function for sortableThemeBootStrap · c2d14321
  Ruben Vorderman authored Jul 24, 2017
  
  c2d14321
- Removed some variables from ssp file. · cf8259b9
  Ruben Vorderman authored Jul 24, 2017
  
  cf8259b9
- Make it possible to disable gubbins · afa1608d
  Peter van 't Hof authored Jul 24, 2017
  
  afa1608d
- Started on flexiprepReadSummary.ssp · e859f656
  Ruben Vorderman authored Jul 24, 2017
  
  e859f656
- Changing name blah ;) · e32832d3
  Peter van 't Hof authored Jul 24, 2017
  
  e32832d3
- Typos · 1c4febed
  Peter van 't Hof authored Jul 24, 2017
  
  1c4febed
- Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-750 · 28db4a1e
  Peter van 't Hof authored Jul 24, 2017
  
  28db4a1e
21 Jul, 2017 4 commits
- Added shiva report to Basty · 9c297111
  Peter van 't Hof authored Jul 21, 2017
  
  9c297111
- Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-718 · dd937c3a
  Peter van 't Hof authored Jul 21, 2017
  
  dd937c3a
- Fixed path in stats.json · e70a3c2e
  Peter van 't Hof authored Jul 21, 2017
  
  e70a3c2e
- Merge pull request #159 from biopet/fix-BIOPET-736-peter · 9b83c7aa
  Peter van 't Hof authored Jul 21, 2017
```
Adding documentation for mutect2
```
  9b83c7aa