Commits · 9002b6ce09b1d31a19816fffb84af2ffdb611087 · Mirrors / biopet.biopet

Nov 03, 2015
- Fixed gears parsing · 9002b6ce
  Peter van 't Hof authored 9 years ago
  
  9002b6ce
Nov 02, 2015
- Added sunburst plot to mapping and shiva · 89bc7d9a
  Peter van 't Hof authored 9 years ago
  
  89bc7d9a
Oct 31, 2015
- Added sample / lib to report · 9ac622a9
  Peter van 't Hof authored 9 years ago
  
  9ac622a9
Oct 30, 2015
- Optimize code · 3cd8150f
  Peter van 't Hof authored 9 years ago
  
  3cd8150f
- Added input file checking · 20cd7b6d
  Peter van 't Hof authored 9 years ago
  
  20cd7b6d
Oct 29, 2015
- Simplify unmapped reads extraction · b7743a6e
  Wai Yi Leung authored 9 years ago
  
  b7743a6e
- Fix resource copy for the report · 972ad0f3
  Wai Yi Leung authored 9 years ago
  
  972ad0f3
- Fixed summary file name · 2f92eb6d
  Peter van 't Hof authored 9 years ago
  
  2f92eb6d
- change pipeline test, not test on sambambaview, but on samtoolsview · 11fe02b4
  Wai Yi Leung authored 9 years ago
  
  11fe02b4
- More style fixes · 755b864d
  Wai Yi Leung authored 9 years ago
  
  755b864d
- Remove sambamba and use samtools for extracting pairs of unmapped reads (not the advanced query) · 6483fd1f
  Wai Yi Leung authored 9 years ago
  
  6483fd1f
- Style fixes and config for samtofastq · 705d9cd6
  Wai Yi Leung authored 9 years ago
  
  705d9cd6
Oct 28, 2015
- Refactor the report generation a bit. Move pipeline specific report components... · 4c405315
  Wai Yi Leung authored 9 years ago
  
  Refactor the report generation a bit. Move pipeline specific report components into the pipeline itself (not hosted in core anymore)
  4c405315
- Fixes for the comments made in the ticket #241 · 1b673dfa
  Wai Yi Leung authored 9 years ago
  
  1b673dfa
Oct 27, 2015
- Code style fixes · 41eade8b
  Peter van 't Hof authored 9 years ago
  
  41eade8b
Oct 22, 2015
- Bugfix in KrakenReportToJson, include Root and Unclassified in any case. · 0f4f1881
  Wai Yi Leung authored 9 years ago
  
  0f4f1881
- POM definition fix. · 3ded0090
  Wai Yi Leung authored 9 years ago
  
  3ded0090
- Adding tests for Gears · 1adc4916
  Wai Yi Leung authored 9 years ago
  
  1adc4916
- Small fixes in report · 627f9574
  Wai Yi Leung authored 9 years ago
  
  627f9574
Oct 21, 2015
- Fix markup in code · 73033e0d
  Wai Yi Leung authored 9 years ago
  
  Reorganize output json, including unclassified readcount
  73033e0d
Oct 20, 2015
- Report update · 36f70f66
  Wai Yi Leung authored 9 years ago
  
  36f70f66
Oct 19, 2015
- Adjusting the Sambamba view filter, exclude "split reads" in RNA-seq experiments · 5d18d629
  Wai Yi Leung authored 9 years ago
  
  5d18d629
- Style update by IDEA · caf77b81
  Wai Yi Leung authored 9 years ago
  
  caf77b81
- Updated krakentojson report and enforce check-names with-in Kraken · d82b56a0
  Wai Yi Leung authored 9 years ago
  
  d82b56a0
- Handle RNA seq files, sam filter only takes the primary alignment · ceaa8fd0
  Wai Yi Leung authored 9 years ago
  
  ceaa8fd0
Oct 14, 2015
- Output singleton reads (in case the input bam had dedup with removal turned on) · b4a13e74
  Wai Yi Leung authored 9 years ago
  
  b4a13e74
Oct 06, 2015
- Adding files to summary json · 4350c5b5
  Wai Yi Leung authored 9 years ago
  
  4350c5b5
Oct 05, 2015
- Add extension wrapper for biopet, Allow to skipNames in reporting for concise... · b674053a
  Wai Yi Leung authored 9 years ago
  
  Add extension wrapper for biopet, Allow to skipNames in reporting for concise report containing only counts and taxonID's
  b674053a
Oct 02, 2015
- Adding krakenreport2json to gears pipeline · 6f58b7e2
  Wai Yi Leung authored 9 years ago
  
  6f58b7e2
Sep 29, 2015
- Switch to fifo pipes · 8ae539f7
  Peter van 't Hof authored 9 years ago
  
  8ae539f7
- Add todo to GEARS pipeline. · 72aa3362
  Wai Yi Leung authored 9 years ago
  
  72aa3362
Sep 24, 2015
- removed qscript key · c15b307b
  Peter van 't Hof authored 9 years ago
  
  c15b307b
- Refactoring of gears · bbc185f4
  Peter van 't Hof authored 9 years ago
  
  bbc185f4
Sep 23, 2015
- Added support to have a pipe as input file · f298fe2c
  Peter van 't Hof authored 9 years ago
  
  f298fe2c
Sep 13, 2015
- Fix pipeline without framework · f3343df9
  Peter van 't Hof authored 9 years ago
  
  f3343df9
Sep 10, 2015
- Moved config to utils · a81bce67
  Peter van 't Hof authored 9 years ago
  
  a81bce67
Sep 04, 2015
- Changing to SNAPSHOT version, this is following the maven convention · f550b637
  Peter van 't Hof authored 9 years ago
  
  f550b637
Aug 03, 2015
- Review changes · e667ee49
  Peter van 't Hof authored 9 years ago
  
  e667ee49
- Removed the trait, no need for it · bc53f7e3
  Peter van 't Hof authored 9 years ago
  
  bc53f7e3
Jul 30, 2015
- Bumb version to 0.5.0-DEV · c3b83b90
  Peter van 't Hof authored 9 years ago
  
  c3b83b90