Commits · 6d607d944bed64efce73d7883ec5e2cabd3810c5 · Mirrors / biopet.biopet

16 Mar, 2015 6 commits
- More generic pipeline names · 6d607d94
  Peter van 't Hof authored Mar 16, 2015
  
  6d607d94
- Convert docs for shiva · 0cc8977b
  Peter van 't Hof authored Mar 16, 2015
  
  0cc8977b
- Update SAGE documentation · 35c4b240
  bow authored Mar 16, 2015
  
  35c4b240
- Update GSNAP wrapper memory · 6601f23d
  bow authored Mar 16, 2015
  
  6601f23d
- Fix memory requirements · 84f861ec
  Peter van 't Hof authored Mar 16, 2015
  
  84f861ec
- Rename VEPNormalizer -> VepNormalizer for consistency · 8f59db2c
  bow authored Mar 16, 2015
  
  8f59db2c
15 Mar, 2015 3 commits
- Update main executable pipelines and tool visibility · ff74a677
  bow authored Mar 15, 2015
  
  ff74a677
- Docs updates · 47b5dd69
  bow authored Mar 15, 2015
  
  47b5dd69
- Set default GSNAP vmem for GSNAP wrapper · e02dc9dc
  bow authored Mar 15, 2015
  
  e02dc9dc
14 Mar, 2015 2 commits
- fix args name in queue extension · c684c318
  Peter van 't Hof authored Mar 14, 2015
  
  c684c318
- Fix args in queue extension · 6f07dcdc
  Peter van 't Hof authored Mar 14, 2015
  
  6f07dcdc
13 Mar, 2015 24 commits
- Bump version to 0.3.0 · c5e27ef2
  bow authored Mar 13, 2015
  
  c5e27ef2
- Update mkdocs.yml · 319f4fb3
  bow authored Mar 13, 2015
  
  319f4fb3
- Merge branch 'docs-toucan' into 'release-0.3.0' · aa04f501
  bow authored Mar 13, 2015
```
Docs toucan

See merge request !133
```
  aa04f501
- Update Gentrap docs · bb337946
  bow authored Mar 13, 2015
  
  bb337946
- adding toucan to docs · a141edb3
  Sander Bollen authored Mar 13, 2015
  
  a141edb3
- adding VEPNormalizer to docs · 9c0459c7
  Sander Bollen authored Mar 13, 2015
  
  9c0459c7
- Update index page · a4fb8a3d
  bow authored Mar 13, 2015
  
  a4fb8a3d
- Update about page · d16ce249
  bow authored Mar 13, 2015
  
  d16ce249
- Merge branch 'docs_v.0.3.0' into release-0.3.0 · 7c333019
  bow authored Mar 13, 2015
  
  7c333019
- Flip order or reporting to show later results first · 635feee0
  bow authored Mar 13, 2015
  
  635feee0
- Fix variable name error in report template generator · 81ca7f7e
  bow authored Mar 13, 2015
  
  81ca7f7e
- Add missing CollectRnaSeqMetrics values · 13647e73
  bow authored Mar 13, 2015
  
  13647e73
- Fix wrong Picard class for Picard ReorderSam · 40276768
  bow authored Mar 13, 2015
  
  40276768
- Use correct directory for checking dict file in Gentrap · 1fb00ca7
  bow authored Mar 13, 2015
  
  1fb00ca7
- Update Gentrap dict test to be more test-friendly · bbbaecd3
  bow authored Mar 13, 2015
  
  bbbaecd3
- Formatting updates · 2139a95e
  bow authored Mar 13, 2015
  
  2139a95e
- Add check to ensure dict file is present in Gentrap · 0453d301
  bow authored Mar 13, 2015
  
  0453d301
- Ensure GSNAP output has the same ordering as reference FASTA · 80b0cbcc
  bow authored Mar 13, 2015
  
  80b0cbcc
- Add ReorderSam (to ensure correct sam header ordering) · ee058d6a
  bow authored Mar 13, 2015
  
  ee058d6a
- Update default Cufflinks vmem · 119ff147
  bow authored Mar 13, 2015
  
  119ff147
- Ensure TopHat keeps index contig order when aligning · fb90d825
  bow authored Mar 13, 2015
  
  fb90d825
- Set default cutadapt minimum_length to 20 in Gentrap · 6ffdacf9
  bow authored Mar 13, 2015
  
  6ffdacf9
- Use correct flag annotations for Picard CollectRnaSeqMetrics · a7b9890f
  bow authored Mar 13, 2015
  
  a7b9890f
- Merge branch 'fixje' into 'release-0.3.0' · 80353a70
  bow authored Mar 13, 2015
```
Fixje

sorry for the many merge requests ;-)

See merge request !132
```
  80353a70
12 Mar, 2015 5 commits
- tiny fix for output directory in bammetrics (no longer outputs stuff in bed input dir) · 0eae2e93
  Sander Bollen authored Mar 12, 2015
  
  0eae2e93
- Merge branch 'fix-vep_normalizer' into 'release-0.3.0' · 7a797196
  bow authored Mar 12, 2015
```
Fix vep normalizer

fix on output of normalizer

See merge request !129
```
  7a797196
- Merge branch 'patch-shiva' into 'release-0.3.0' · 9bb14daa
  bow authored Mar 12, 2015
```
Patch shiva

See merge request !131
```
  9bb14daa
- Set default h_vmem to 6GB for bedtools coverage (used ~3.5GB in test run) · e0ed3259
  Sander Bollen authored Mar 12, 2015
  
  e0ed3259
- Fix BamMetrics to use file in stead of directory · 9d86b1ed
  Sander Bollen authored Mar 12, 2015
```
Fix markduplicates to not overwrite bam file with metrics file
```
  9d86b1ed