Commits · 8b557e11c244ece5d6822b6ab77c644819db4509 · Mirrors / biopet.biopet

28 Jul, 2014 3 commits
- Merge origin/master into peter · 8b557e11
  Peter van 't Hof authored Jul 28, 2014
  
  8b557e11
- Merge branch 'bow' · 8a830d49
  bow authored Jul 28, 2014
  
  8a830d49
- Add cutadapt statistics output to flexiprep runs · d3a453a1
  bow authored Jul 28, 2014
  
  d3a453a1
27 Jul, 2014 4 commits
- First version of summary of flexiprep in queue/scala · e6f07f76
  Peter van 't Hof authored Jul 27, 2014
  
  e6f07f76
- Function to get encoding of the fastq file, replaces python script · 2a2a37fd
  Peter van 't Hof authored Jul 27, 2014
  
  2a2a37fd
- Fix on output variable · 096d8a0e
  Peter van 't Hof authored Jul 27, 2014
  
  096d8a0e
- - Moved constructor to function itself · 16a08dfd
  Peter van 't Hof authored Jul 27, 2014
```
- Add extract option to fastqc
```
  16a08dfd
24 Jul, 2014 1 commit
- Add git pre-commit hook script · 748d9525
  bow authored Jul 24, 2014
  
  748d9525
23 Jul, 2014 7 commits
- Update seqtk wrapper docs and formatting · 2c14276c
  bow authored Jul 23, 2014
  
  2c14276c
- Add initial wrapper for seqtk · a7522c76
  bow authored Jul 23, 2014
  
  a7522c76
- Update style settings · f15bfd77
  bow authored Jul 23, 2014
  
  f15bfd77
- Update Sickle wrapper for consistency · d58df8a4
  bow authored Jul 23, 2014
  
  d58df8a4
- Update imports style order · bf372d9a
  bow authored Jul 23, 2014
  
  bf372d9a
- Update code style using scalariform · 02b571a4
  bow authored Jul 23, 2014
  
  02b571a4
- Add style preferences for scalariform · 96ccc270
  bow authored Jul 23, 2014
  
  96ccc270
22 Jul, 2014 2 commits
- Switch to Argonaut library · 7ef47a09
  Peter van 't Hof authored Jul 22, 2014
  
  7ef47a09
- Changes in config class · 6294de9f
  Peter van 't Hof authored Jul 22, 2014
  
  6294de9f
21 Jul, 2014 8 commits
- Changed path to Biopet · 385bfef9
  Peter van 't Hof authored Jul 21, 2014
  
  385bfef9
- Added stand_call_conf and stand_emit_conf option · 7734a3c0
  Peter van 't Hof authored Jul 21, 2014
  
  7734a3c0
- Added stand_call_conf and stand_emit_conf option · 9a25fc2b
  Peter van 't Hof authored Jul 21, 2014
  
  9a25fc2b
- Added Alignment Metrics · 1df0bfa4
  Peter van 't Hof authored Jul 21, 2014
  
  1df0bfa4
- Fixed location of jar file · 89926ccd
  Peter van 't Hof authored Jul 21, 2014
  
  89926ccd
- Spelling error · 95ba716f
  Peter van 't Hof authored Jul 21, 2014
  
  95ba716f
- Collected all gatk pipelines/artifacts into 1 maven project · 2f47af7e
  Peter van 't Hof authored Jul 21, 2014
  
  2f47af7e
- Collected all gatk pipelines/artifacts into 1 maven project · 79435a29
  Peter van 't Hof authored Jul 21, 2014
  
  79435a29
18 Jul, 2014 9 commits
- Fix for outputDir · bffb8a1b
  Peter van 't Hof authored Jul 18, 2014
  
  bffb8a1b
- Fix for Queue-3.2-2 · 94c23ca3
  Peter van 't Hof authored Jul 18, 2014
  
  94c23ca3
- Added 2 modules · 9be6e744
  Peter van 't Hof authored Jul 18, 2014
  
  9be6e744
- Added a benchmark pipeline for gvcf · ea95c71d
  Peter van 't Hof authored Jul 18, 2014
  
  ea95c71d
- Added GatkPipeline, finaly replacement for "Gatk" pipeline · f49e6275
  Peter van 't Hof authored Jul 18, 2014
  
  f49e6275
- Added min_mapping_quality_score to haplotypecaller · ae952d4c
  Peter van 't Hof authored Jul 18, 2014
  
  ae952d4c
- update for Queue/GATK 3.2-2 · 62ed4c90
  Peter van 't Hof authored Jul 18, 2014
  
  62ed4c90
- update for Queue/GATK 3.2-2 · 3b0a7242
  Peter van 't Hof authored Jul 18, 2014
  
  3b0a7242
- Library fix for Queue/GATK 3.2 · 044fe79f
  Peter van 't Hof authored Jul 18, 2014
  
  044fe79f
15 Jul, 2014 6 commits
- Merge branch 'patch_readme' into 'master' · 398500a6
  Peter van 't Hof authored Jul 15, 2014
```
README updates

README updates with installation notes (includes non-SHARK and SHARK installs)
```
  398500a6
- Update to Queue/GATK 3.2 · 0a33b3d3
  Peter van 't Hof authored Jul 15, 2014
  
  0a33b3d3
- Update README with installation notes · 90bfd70e
  bow authored Jul 15, 2014
  
  90bfd70e
- Summary is skipped in chunking mode · 719894d1
  Peter van 't Hof authored Jul 15, 2014
  
  719894d1
- intial unzipped file is intermediate now · 2e45f064
  Peter van 't Hof authored Jul 15, 2014
  
  2e45f064
- Added a module for Genotyping · 43881d8d
  Peter van 't Hof authored Jul 15, 2014
  
  43881d8d