Commits · 000989d73eb035a96bd8df3da536b2cf04fcae9f · Mirrors / biopet.biopet

05 Mar, 2015 14 commits
- Possible to not convert executable to CanonicalPath · 000989d7
  Peter van 't Hof authored Mar 05, 2015
  
  000989d7
- 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
- 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
- Update wrapper for PDF template writer · dd732326
  bow authored Mar 05, 2015
  
  dd732326
- Update base gentrap test with required config value defined · df0760f8
  bow authored Mar 05, 2015
  
  df0760f8
- Move PDF templates to another directory · 53a6b61e
  bow authored Mar 05, 2015
  
  53a6b61e
- Formatting updates · df9dfa59
  bow authored Mar 05, 2015
  
  df9dfa59
04 Mar, 2015 26 commits
- Add pdf report generator wrapper · d6ffd898
  bow authored Mar 04, 2015
  
  d6ffd898
- Add PDF report templates · 47bdab9b
  bow authored Mar 04, 2015
  
  47bdab9b
- Modify pdf_report.py with new base layout · 586c9070
  bow authored Mar 04, 2015
  
  586c9070
- Add templates for plotting scripts and their wrappers · 4cd2f2d5
  bow authored Mar 04, 2015
  
  4cd2f2d5
- Disable untested expMeasure modes · b660ab1c
  bow authored Mar 04, 2015
  
  b660ab1c
- Expose enum-based config values as public attributes · 6b22cc16
  bow authored Mar 04, 2015
  
  6b22cc16
- Formatting updates · 32816835
  bow authored Mar 04, 2015
  
  32816835
- Add variant calling jobs and expose its output as attribute and in summary · 062f17b7
  bow authored Mar 04, 2015
  
  062f17b7
- Add extension for simple RNA variant calling · bcbed83b
  bow authored Mar 04, 2015
  
  bcbed83b
- Add fix_mpileup.py script for VarScan · d50e14ee
  bow authored Mar 04, 2015
  
  d50e14ee
- Add VarScan mpileup2cns wrapper · bf8743a5
  bow authored Mar 04, 2015
  
  bf8743a5
- Add VarScan base wrapper · 6c9acc21
  bow authored Mar 04, 2015
  
  6c9acc21
- Add default value to SamtoolsMpileup.disableBaq · 45d375fd
  bow authored Mar 04, 2015
  
  45d375fd
- Add -s and -d flag to SamtoolsMpileup · 6d0bbf4c
  bow authored Mar 04, 2015
  
  6d0bbf4c
- Initial tabix wrapper · 95462555
  bow authored Mar 04, 2015
  
  95462555
- Add GatherBamFiles wrapper · 882f9e33
  bow authored Mar 04, 2015
  
  882f9e33
- Fix bug that omits md5sum calculation of Flexiprep files · f6cb0ae0
  bow authored Mar 04, 2015
  
  f6cb0ae0
- Use GatherBam for merging per-strand jobs · a6223c3b
  bow authored Mar 04, 2015
  
  a6223c3b
- Use correct conditional for optional strand-specific jobs · 0353a74f
  bow authored Mar 04, 2015
  
  0353a74f
- Use correct flag repetition for SamtoolsView · 49a122e8
  bow authored Mar 04, 2015
  
  49a122e8
- Add strand-specific jobs · 87141e4a
  bow authored Mar 04, 2015
  
  87141e4a
- Properly enclose outputs in RawBaseCounter · 77a04b4b
  bow authored Mar 04, 2015
  
  77a04b4b
- Rename Ln.out => Ln.output and Ln.in => Ln.input · 7eae47d3
  bow authored Mar 04, 2015
  
  7eae47d3
- Add isoforms output to summary · a3e87679
  bow authored Mar 04, 2015
  
  a3e87679
- Add wrapper for bgzip · ba3e1de5
  bow authored Mar 04, 2015
  
  ba3e1de5
- Remove default value from expressionMeasures option · 0b6eb747
  bow authored Mar 04, 2015
  
  0b6eb747