Commits · c69801646fab606358470757dfe90eb383ba3cc5 · Mirrors / biopet.biopet

Sep 28, 2015
- Moved code · c6980164
  Peter van 't Hof authored 9 years ago
  
  c6980164
Sep 27, 2015
- Hide null pointen from unit tests · beef0cec
  Peter van 't Hof authored 9 years ago
  
  beef0cec
- Fixed single-end runs · 6bad7eaf
  Peter van 't Hof authored 9 years ago
  
  6bad7eaf
- Overrider default shell from queue · 41857e5d
  Peter van 't Hof authored 9 years ago
  
  41857e5d
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
- Fix import · 36fd8269
  Peter van 't Hof authored 9 years ago
  
  36fd8269
- 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
- Remove intermediate · 2387d560
  Peter van 't Hof authored 9 years ago
  
  2387d560
- Fixed output pipeline · e40baa30
  Peter van 't Hof authored 9 years ago
  
  e40baa30
Sep 22, 2015
- Better memory handling for pipes · 2ada4499
  Peter van 't Hof authored 9 years ago
  
  2ada4499
- Remove old code · 2da7887f
  Peter van 't Hof authored 9 years ago
  
  2da7887f
- Adding classpath and memory to beforeGraph · 650352d4
  Peter van 't Hof authored 9 years ago
  
  650352d4
- Convert mapping to sortsam for pipes · a952d8c4
  Peter van 't Hof authored 9 years ago
  
  a952d8c4
- Convert pipe to SortSam again · 9a3356a5
  Peter van 't Hof authored 9 years ago
  
  9a3356a5
- Change temp files · 0c43aaf3
  Peter van 't Hof authored 9 years ago
  
  0c43aaf3
- Fix compile errors · 13689911
  Peter van 't Hof authored 9 years ago
  
  13689911
- Moved sam file · bb300878
  Peter van 't Hof authored 9 years ago
  
  bb300878
- style change · 4abe2a58
  Peter van 't Hof authored 9 years ago
  
  4abe2a58
- Added a sum of memory and threads · 1b0093ff
  Peter van 't Hof authored 9 years ago
  
  1b0093ff
- Added the -T arg · 71426017
  Peter van 't Hof authored 9 years ago
  
  71426017
- Added executable to command · ce85fe0a
  Peter van 't Hof authored 9 years ago
  
  ce85fe0a
- Use piping after bwamem · f7ea04a7
  Peter van 't Hof authored 9 years ago
  
  f7ea04a7
- Made output of bwamem pipeable · 93724710
  Peter van 't Hof authored 9 years ago
  
  93724710
- Added samtools sort · b17079d8
  Peter van 't Hof authored 9 years ago
  
  b17079d8
- Made codeMemory readable from outside · 3482754f
  Peter van 't Hof authored 9 years ago
  
  3482754f
Sep 21, 2015
- This will remove tempfiles on exit · 2fdf69e7
  Peter van 't Hof authored 9 years ago
  
  2fdf69e7
- Still executes multisample jobs when all samples are given with --sample flag · fc2af339
  Peter van 't Hof authored 9 years ago
  
  fc2af339
- Fix summary when --sample flag is used in multisample pipelines · ad73824f
  Peter van 't Hof authored 9 years ago
  
  ad73824f
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
- Add comment · a87e2991
  Peter van 't Hof authored 9 years ago
  
  a87e2991
- Fixed case class · bd6eae2c
  Peter van 't Hof authored 9 years ago
  
  bd6eae2c
- Change name · b21fac92
  Peter van 't Hof authored 9 years ago
  
  b21fac92
- Add input files to pipelines · 4875e508
  Peter van 't Hof authored 9 years ago
  
  4875e508