Commits · bbbaecd3b3990deab4dc58e64597b8313a2fb3a6 · Mirrors / biopet.biopet

Mar 13, 2015
- Update Gentrap dict test to be more test-friendly · bbbaecd3
  bow authored 10 years ago
  
  bbbaecd3
- Formatting updates · 2139a95e
  bow authored 10 years ago
  
  2139a95e
- Add check to ensure dict file is present in Gentrap · 0453d301
  bow authored 10 years ago
  
  0453d301
- Ensure GSNAP output has the same ordering as reference FASTA · 80b0cbcc
  bow authored 10 years ago
  
  80b0cbcc
- Add ReorderSam (to ensure correct sam header ordering) · ee058d6a
  bow authored 10 years ago
  
  ee058d6a
- Update default Cufflinks vmem · 119ff147
  bow authored 10 years ago
  
  119ff147
- Ensure TopHat keeps index contig order when aligning · fb90d825
  bow authored 10 years ago
  
  fb90d825
- Set default cutadapt minimum_length to 20 in Gentrap · 6ffdacf9
  bow authored 10 years ago
  
  6ffdacf9
- Use correct flag annotations for Picard CollectRnaSeqMetrics · a7b9890f
  bow authored 10 years ago
  
  a7b9890f
- Merge branch 'fixje' into 'release-0.3.0' · 80353a70
  bow authored 10 years ago
  
  Fixje sorry for the many merge requests ;-) See merge request !132
  80353a70
Mar 12, 2015
- tiny fix for output directory in bammetrics (no longer outputs stuff in bed input dir) · 0eae2e93
  Sander Bollen authored 10 years ago
  
  0eae2e93
- Merge branch 'fix-vep_normalizer' into 'release-0.3.0' · 7a797196
  bow authored 10 years ago
  
  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 10 years ago
  
  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 10 years ago
  
  e0ed3259
- Fix BamMetrics to use file in stead of directory · 9d86b1ed
  Sander Bollen authored 10 years ago
  
  Fix markduplicates to not overwrite bam file with metrics file
  9d86b1ed
- Fix format and typo's · da93f0ca
  Peter van 't Hof authored 10 years ago
  
  da93f0ca
- added counter · 9a2c81d5
  Peter van 't Hof authored 10 years ago
  
  9a2c81d5
- Default to disabling MarkDuplicates in Gentrap · 0267b656
  bow authored 10 years ago
  
  0267b656
- Fix threads allocation to GSNAP, TopHat, and Cufflinks wrappers · 16422010
  bow authored 10 years ago
  
  16422010
Mar 11, 2015
- Fix output of normalizer · 7dafdb1b
  Peter van 't Hof authored 10 years ago
  
  7dafdb1b
- Fix test failure caused by incorrectly named function · aa8fe3fd
  bow authored 10 years ago
  
  aa8fe3fd
- Add more descriptive error message in Carp when sample is called control · 675718da
  bow authored 10 years ago
  
  675718da
- Fix missing metrics accumulation level default value · ad297734
  bow authored 10 years ago
  
  ad297734
- Update requirement message in Shiva · fb67d765
  bow authored 10 years ago
  
  fb67d765
- Update licenses · 3ec60672
  bow authored 10 years ago
  
  3ec60672
- Bump version to 0.3.0-RC1 · a289c540
  bow authored 10 years ago
  
  a289c540
- Fix missing read group assignment for GSNAP and TopHat · cfd74de0
  bow authored 10 years ago
  
  cfd74de0
- Merge branch 'patch-bam2wig' into 'develop' · 68d7fab7
  bow authored 10 years ago
  
  Patch bam2wig See merge request !128
  68d7fab7
- changed .bigwig extension to .bw · d9e2a1e2
  Sander van der Zeeuw authored 10 years ago
  
  d9e2a1e2
- Merge branch 'patch-toucan' into 'develop' · 99cc75c4
  bow authored 10 years ago
  
  Patch toucan This enables to `--fork` command of the VEP to actually run with Biopet's `-qsub` command. See merge request !126
  99cc75c4
- removing commented out lines · 7059cf76
  Sander Bollen authored 10 years ago
  
  7059cf76
- threads in VEP wrapper for Toucan · 3ff984dd
  Sander Bollen authored 10 years ago
  
  3ff984dd
- Merge branch 'feature-gentrap' into 'develop' · 4387eae8
  Wai Yi Leung authored 10 years ago
  
  Feature gentrap See merge request !111
  4387eae8
Mar 10, 2015
- Various fixes for cluster compatibility · 41f9df22
  bow authored 10 years ago
  
  41f9df22
- Merge branch 'develop' into feature-gentrap · 6c394efd
  bow authored 10 years ago
  
  6c394efd
- Merge branch 'patch-genotyper' into 'develop' · b4acd8fd
  bow authored 10 years ago
  
  Patch genotyper Fix a small bug on unified genotyper See merge request !125
  b4acd8fd
- Fix scattercounts · 7a573705
  Peter van 't Hof authored 10 years ago
  
  7a573705
- Ensure correct config name · 4521305b
  bow authored 10 years ago
  
  4521305b
- More missing executables config · 32796b57
  bow authored 10 years ago
  
  32796b57
- Add missing mock executable for testing · 3a1f0235
  bow authored 10 years ago
  
  3a1f0235