Commits · c5e27ef20976050f5d4088223e0367f192a51a49 · Mirrors / biopet.biopet

Mar 13, 2015
- Bump version to 0.3.0 · c5e27ef2
  bow authored 10 years ago
  
  c5e27ef2
- Flip order or reporting to show later results first · 635feee0
  bow authored 10 years ago
  
  635feee0
- Fix variable name error in report template generator · 81ca7f7e
  bow authored 10 years ago
  
  81ca7f7e
- Add missing CollectRnaSeqMetrics values · 13647e73
  bow authored 10 years ago
  
  13647e73
- Fix wrong Picard class for Picard ReorderSam · 40276768
  bow authored 10 years ago
  
  40276768
- Use correct directory for checking dict file in Gentrap · 1fb00ca7
  bow authored 10 years ago
  
  1fb00ca7
- 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
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
- 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
- changed .bigwig extension to .bw · d9e2a1e2
  Sander van der Zeeuw authored 10 years ago
  
  d9e2a1e2
- 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
Mar 10, 2015
- Various fixes for cluster compatibility · 41f9df22
  bow authored 10 years ago
  
  41f9df22
- 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
- Add missing mock bam2wig executables in GentrapTest · 0109059c
  bow authored 10 years ago
  
  0109059c
- Fix wrong Cufflinks threads · e459cf6e
  bow authored 10 years ago
  
  e459cf6e
- Fix wrong threads setting in Star wrapper · bfa58fe2
  bow authored 10 years ago
  
  bfa58fe2