Commits · 6af004167ea86765411af823909b2e3423998568 · Mirrors / biopet.biopet

Oct 19, 2015
- Use provided exts Set instead of zipExtensions · 6af00416
  bow authored 9 years ago
  
  6af00416
- Remove R1_ext and R2_ext from Flexiprep · 90eaaf09
  bow authored 9 years ago
  
  90eaaf09
- Add error message when a Flexiprep input file does not have the expected structure · 487324b4
  bow authored 9 years ago
  
  487324b4
- Refactor filename and extension retrieval in Flexiprep · b4b6785a
  bow authored 9 years ago
  
  b4b6785a
Oct 09, 2015
- Fix zcat for chunking · ca9c7e5c
  Peter van 't Hof authored 9 years ago
  
  ca9c7e5c
- Fix chunking · f4f1f4cb
  Peter van 't Hof authored 9 years ago
  
  f4f1f4cb
Oct 06, 2015
- Fixed tests in flexiprep · 95ae061e
  Peter van 't Hof authored 9 years ago
  
  95ae061e
- Always execute fastqc_qc · 85f7eb91
  Peter van 't Hof authored 9 years ago
  
  85f7eb91
- Added adapters to summary · 2d241e33
  Peter van 't Hof authored 9 years ago
  
  2d241e33
Oct 05, 2015
- Removed out commented tests · b733ff34
  Peter van 't Hof authored 9 years ago
  
  b733ff34
- Remove useless lines · 31822f0a
  Peter van 't Hof authored 9 years ago
  
  31822f0a
- Fix single end dependency · 936e77a0
  Peter van 't Hof authored 9 years ago
  
  936e77a0
Oct 02, 2015
- Fix code style warnings · 52928227
  Peter van 't Hof authored 9 years ago
  
  52928227
- Move input for gzip to stdin to not remove file · 2156f192
  Peter van 't Hof authored 9 years ago
  
  2156f192
- Fixed summary files of flexiprep · 5d5c30c1
  Peter van 't Hof authored 9 years ago
  
  5d5c30c1
Sep 30, 2015
- Removed test · 310b07ef
  Peter van 't Hof authored 9 years ago
  
  310b07ef
Sep 29, 2015
- Switch to fifo pipes · 8ae539f7
  Peter van 't Hof authored 9 years ago
  
  8ae539f7
Sep 28, 2015
- Changed own vmem · adb6ffe1
  Peter van 't Hof authored 9 years ago
  
  adb6ffe1
- Adding summary stats · f42be845
  Peter van 't Hof authored 9 years ago
  
  f42be845
- Fixed resources · 6fc77a78
  Peter van 't Hof authored 9 years ago
  
  6fc77a78
Sep 27, 2015
- Fixed single-end runs · 6bad7eaf
  Peter van 't Hof authored 9 years ago
  
  6bad7eaf
Sep 25, 2015
- Added deps · 5096c156
  Peter van 't Hof authored 9 years ago
  
  5096c156
- Fix fastqc dependency · 206c7f01
  Peter van 't Hof authored 9 years ago
  
  206c7f01
- Fixed QcCommand · 7a3bf3b2
  Peter van 't Hof authored 9 years ago
  
  7a3bf3b2
Sep 24, 2015
- Added FilePipes · 04210893
  Peter van 't Hof authored 9 years ago
  
  04210893
Sep 23, 2015
- Added support to have a pipe as input file · f298fe2c
  Peter van 't Hof authored 9 years ago
  
  f298fe2c
- Remove count tests · 839b0c12
  Peter van 't Hof authored 9 years ago
  
  839b0c12
- Refactor flexiprep, more pipes are used now · c6c7c899
  Peter van 't Hof authored 9 years ago
  
  c6c7c899
- Adding a QC command · 8e950ef8
  Peter van 't Hof authored 9 years ago
  
  8e950ef8
Sep 18, 2015
- Fixed unit tests · 6c7f4701
  Peter van 't Hof authored 9 years ago
  
  6c7f4701
- Fastq sync is not intermediate · 884125eb
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit 5f7b2cbe)
  884125eb
- Fixed case class · bd6eae2c
  Peter van 't Hof authored 9 years ago
  
  bd6eae2c
- Fastq sync is not intermediate · 5f7b2cbe
  Peter van 't Hof authored 9 years ago
  
  5f7b2cbe
- Adding input files to check · 3c83721a
  Peter van 't Hof authored 9 years ago
  
  3c83721a
Sep 17, 2015
- Fixed qc stats in report · ac12d5a9
  Peter van 't Hof authored 9 years ago
  
  ac12d5a9
Sep 14, 2015
- style changes · 643418a2
  Peter van 't Hof authored 9 years ago
  
  643418a2
Sep 13, 2015
- Fix pipeline without framework · f3343df9
  Peter van 't Hof authored 9 years ago
  
  f3343df9
- Rscript usable without core now · 7d112c68
  Peter van 't Hof authored 9 years ago
  
  7d112c68
Sep 11, 2015
- Tools split into new modules, core and utils are compileable now · eb97957f
  Peter van 't Hof authored 9 years ago
  
  eb97957f
Sep 10, 2015
- Moved config to utils · a81bce67
  Peter van 't Hof authored 9 years ago
  
  a81bce67