Commits · d2efef6d40588ff7f60f378cc87be378d751f0bc · Mirrors / biopet.biopet

Mar 19, 2015
- Bump version from 0.3.0 to 0.3.1 · d2efef6d
  Wai Yi Leung authored 10 years ago
  
  d2efef6d
- Also change dependency for cutadept · fdeace11
  Peter van 't Hof authored 10 years ago and Wai Yi Leung committed 10 years ago
  
  (cherry picked from commit 6459b271)
  fdeace11
- Fix dependency bug in flexiprep · c1834fcf
  Peter van 't Hof authored 10 years ago and Wai Yi Leung committed 10 years ago
  
  (cherry picked from commit 95db7a53)
  c1834fcf
- Fix incorrectly passed java flags for piped VarScan command · d215796c
  bow authored 10 years ago and Wai Yi Leung committed 10 years ago
  
  (cherry picked from commit f4d7e851)
  d215796c
Mar 16, 2015
- Fir location of count files · 36ddbb2a
  Peter van 't Hof authored 10 years ago
  
  36ddbb2a
- Change file extension for better igv support · 183c3f33
  Peter van 't Hof authored 10 years ago
  
  183c3f33
- Fix on help info for sample arg · 9bdd717f
  Peter van 't Hof authored 10 years ago
  
  9bdd717f
- Update GSNAP wrapper memory · 6601f23d
  bow authored 10 years ago
  
  6601f23d
- Fix memory requirements · 84f861ec
  Peter van 't Hof authored 10 years ago
  
  84f861ec
- Rename VEPNormalizer -> VepNormalizer for consistency · 8f59db2c
  bow authored 10 years ago
  
  8f59db2c
Mar 15, 2015
- Update main executable pipelines and tool visibility · ff74a677
  bow authored 10 years ago
  
  ff74a677
- Set default GSNAP vmem for GSNAP wrapper · e02dc9dc
  bow authored 10 years ago
  
  e02dc9dc
Mar 14, 2015
- fix args name in queue extension · c684c318
  Peter van 't Hof authored 10 years ago
  
  c684c318
- Fix args in queue extension · 6f07dcdc
  Peter van 't Hof authored 10 years ago
  
  6f07dcdc
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