Commits · 66bf4e3ff6e0f3a6c41c9a0f33c6001417bb468f · Mirrors / biopet.biopet

06 Mar, 2015 14 commits
- Fix missing adapter name in flexiprep summary · 66bf4e3f
  bow authored Mar 06, 2015
  
  66bf4e3f
- Add version to gentrap summary output · 2fb27c1b
  bow authored Mar 06, 2015
  
  2fb27c1b
- Formatting updates · 86171153
  bow authored Mar 06, 2015
  
  86171153
- Fix sickle wrapper bug causing by incorrect flag output · 6827c6b5
  bow authored Mar 06, 2015
  
  6827c6b5
- Update test for fragments_per_gene mode · 219ead09
  bow authored Mar 06, 2015
  
  219ead09
- Further trim down tests · 1c953ac1
  bow authored Mar 06, 2015
  
  1c953ac1
- Add convenience methods for creating sample configs · 2d0050ea
  bow authored Mar 06, 2015
  
  2d0050ea
- Trim down general test to test for expMeasure and strandProtocol combinations · c7cd5499
  bow authored Mar 06, 2015
  
  c7cd5499
- Add more config options to test in GentrapTest · 76ef30d0
  bow authored Mar 06, 2015
  
  76ef30d0
- Fix duplicate value on valid cufflinks measures · a207d0b6
  bow authored Mar 06, 2015
  
  a207d0b6
- Remove addAllJobs from CufflinksProducer · 10873179
  bow authored Mar 06, 2015
  
  10873179
- Refactor Cufflinks jobs into its own trait · acdacee9
  bow authored Mar 06, 2015
  
  acdacee9
- Add general heatmap plotting fallback when error is encountered · dbc78f53
  bow authored Mar 06, 2015
  
  dbc78f53
- Rename for consistency · e5dd66c8
  bow authored Mar 06, 2015
  
  e5dd66c8
05 Mar, 2015 26 commits
- Update formatting · 51031007
  bow authored Mar 05, 2015
  
  51031007
- Initial update for GentrapTest · 497eef6f
  bow authored Mar 05, 2015
  
  497eef6f
- Avoid NullPointerException when checking for R2 in Gentrap · e714e45d
  bow authored Mar 05, 2015
  
  e714e45d
- Put all expression table outputs into a single directory · 40eeaa44
  bow authored Mar 05, 2015
  
  40eeaa44
- Add heatmap plot jobs for all output · 393af584
  bow authored Mar 05, 2015
  
  393af584
- Create fallback plot when data points for heatmap is not enough · 307af384
  bow authored Mar 05, 2015
  
  307af384
- Use scalaz's implicit option for boolean · 67ae06c1
  bow authored Mar 05, 2015
  
  67ae06c1
- Initial heat map plotting · e7764348
  bow authored Mar 05, 2015
  
  e7764348
- Update heatmap wrapper · 87396efb
  bow authored Mar 05, 2015
  
  87396efb
- Update heatmap plot sizes · 4f78c3f1
  bow authored Mar 05, 2015
  
  4f78c3f1
- Update heatmap plotting script · 897fbf4e
  bow authored Mar 05, 2015
  
  897fbf4e
- Merge branch 'develop' into feature-gentrap · 7eec6949
  bow authored Mar 05, 2015
  
  7eec6949
- Add job for writing PDF report · 6d78e827
  bow authored Mar 05, 2015
  
  6d78e827
- Merge branch 'patch-executable_check' into 'develop' · 8fbf2803
  bow authored Mar 05, 2015
```
Patch executable check

See merge request !114
```
  8fbf2803
- Possible to not convert executable to CanonicalPath · 000989d7
  Peter van 't Hof authored Mar 05, 2015
  
  000989d7
- Possible to not convert executable to CanonicalPath · 043874a8
  Peter van 't Hof authored Mar 05, 2015
  
  043874a8
- Add initial wrapper for pdflatex · fc509cee
  bow authored Mar 05, 2015
  
  fc509cee
- Pass path to logo to template generator · 5acdef81
  bow authored Mar 05, 2015
  
  5acdef81
- Formatting updates · c55ab605
  bow authored Mar 05, 2015
  
  c55ab605
- Add indexing job to CustomVarScan · 2b9fd392
  bow authored Mar 05, 2015
  
  2b9fd392
- Update Tabix wrapper · 6ca9d8be
  bow authored Mar 05, 2015
  
  6ca9d8be
- Merge branch 'patch-carp' into 'develop' · 27035485
  bow authored Mar 05, 2015
```
Patch carp

Merge to fix the wrong directory of MACS2 single samples runs

See merge request !113
```
  27035485
- Move custom RScript wrapper to Gentrap directory · dd9b9bb9
  bow authored Mar 05, 2015
  
  dd9b9bb9
- Allow custom extensions to have their exes set-up via config · 7dd62911
  bow authored Mar 05, 2015
  
  7dd62911
- Formatting updates · cf117dac
  bow authored Mar 05, 2015
  
  cf117dac
- Add PDF template writing job to main Gentrap · 6f33fef8
  bow authored Mar 05, 2015
  
  6f33fef8