Commits · 449202bdf4f304430916f84ce822f79cf2e2f686 · Mirrors / biopet.biopet

27 Jan, 2015 1 commit
- Remove queue args from pipeline · 449202bd
  Peter van 't Hof authored Jan 27, 2015
  
  449202bd
19 Jan, 2015 1 commit
- Remove unused vars · b3ae6caf
  Peter van 't Hof authored Jan 19, 2015
  
  b3ae6caf
14 Jan, 2015 2 commits
- Remove old script · 1f864153
  Peter van 't Hof authored Jan 14, 2015
  
  1f864153
- Switch to method for adapters · 020ffb1f
  Peter van 't Hof authored Jan 14, 2015
  
  020ffb1f
05 Dec, 2014 1 commit
- Added License to header of all files · b2a02952
  Peter van 't Hof authored Dec 05, 2014
  
  b2a02952
22 Nov, 2014 2 commits
- Added flexiprep as separated artifact · 13430b2e
  Peter van 't Hof authored Nov 22, 2014
  
  13430b2e
- Move BiopetFramework to public maven project · 7d730675
  Peter van 't Hof authored Nov 22, 2014
  
  7d730675
07 Nov, 2014 1 commit
- Change to config · b7952c01
  Peter van 't Hof authored Nov 07, 2014
  
  b7952c01
05 Nov, 2014 1 commit
- Removed config file reading, already done in biopetQScript · 92dc5c59
  Peter van 't Hof authored Nov 05, 2014
  
  92dc5c59
28 Oct, 2014 1 commit
- Build with scaliform · cc8b2760
  Peter van 't Hof authored Oct 28, 2014
  
  cc8b2760
20 Oct, 2014 1 commit
- Removing Python version of seqstat and add the wrapper for the dQual/FastDtools version · 6eec9fed
  wyleung authored Oct 20, 2014
  
  6eec9fed
08 Oct, 2014 1 commit
- Automatic class name conversion · 2c5d1151
  Peter van 't Hof authored Oct 08, 2014
  
  2c5d1151
26 Aug, 2014 1 commit
- Fix on final jobs · bbe9311d
  Peter van 't Hof authored Aug 26, 2014
  
  bbe9311d
25 Aug, 2014 4 commits
- Added Sage pipeline · 1ddd45ad
  Peter van 't Hof authored Aug 25, 2014
  
  1ddd45ad
- Moved scripts to general package · 3c616b75
  Peter van 't Hof authored Aug 25, 2014
  
  3c616b75
- Merge commit 'cfae9015' · 4557807c
  Peter van 't Hof authored Aug 25, 2014
```
Conflicts:
	flexiprep/nbactions.xml
	gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
	gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	mapping/examples/test.json
	mapping/nbactions.xml
	pom.xml
```
  4557807c
- Merge all maven packages into 1 · 7624b929
  Peter van 't Hof authored Aug 25, 2014
  
  7624b929
14 Aug, 2014 1 commit
- Fix on end files on flexiprep, not intermediate anymore · 9d40cb55
  Peter van 't Hof authored Aug 14, 2014
  
  9d40cb55
11 Aug, 2014 3 commits
- Removed unused imports · 48524cb0
  Peter van 't Hof authored Aug 11, 2014
  
  48524cb0
- Output of flexiprep is now a zipped file · d26a67ab
  Peter van 't Hof authored Aug 11, 2014
  
  d26a67ab
- Switch to md5sum · 41fa137b
  Peter van 't Hof authored Aug 11, 2014
  
  41fa137b
08 Aug, 2014 1 commit
- Removed skipsummary option · daf02820
  Peter van 't Hof authored Aug 08, 2014
  
  daf02820
06 Aug, 2014 3 commits
- Removed old summary and fix file name for new summary · 8c8bb2f3
  Peter van 't Hof authored Aug 06, 2014
  
  8c8bb2f3
- Added getSummary function · e469c3ab
  Peter van 't Hof authored Aug 06, 2014
  
  e469c3ab
- Make Sample and library name required · 48431cd5
  Peter van 't Hof authored Aug 06, 2014
  
  48431cd5
04 Aug, 2014 2 commits
- Added SeqtkSeq to flexiprep · 1e3bfb26
  Peter van 't Hof authored Aug 04, 2014
  
  1e3bfb26
- Use of new constructors · 7c1fa255
  Peter van 't Hof authored Aug 04, 2014
  
  7c1fa255
30 Jul, 2014 2 commits
- Wrappers are now split in general and specific flexiprep extensions · 6b5c4320
  Peter van 't Hof authored Jul 30, 2014
  
  6b5c4320
- Style reformatting · 19f47e48
  bow authored Jul 30, 2014
  
  19f47e48
29 Jul, 2014 5 commits
- Fix on output directories of sha1sum and seqstat · 0aabeb73
  bow authored Jul 29, 2014
  
  0aabeb73
- Flexiprep passes jobs to new summary · 397a0a5d
  Peter van 't Hof authored Jul 29, 2014
  
  397a0a5d
- Use relative symlinks by default in Flexiprep final files · deac9640
  bow authored Jul 29, 2014
  
  deac9640
- changed function to extensions · dd4f0175
  Peter van 't Hof authored Jul 29, 2014
  
  dd4f0175
- Seqstat now uses quality type data · 3501d2eb
  Peter van 't Hof authored Jul 28, 2014
  
  3501d2eb
28 Jul, 2014 6 commits
- Seqstat now uses quality type data · 8e67bf4f
  Peter van 't Hof authored Jul 28, 2014
  
  8e67bf4f
- Update flexiprep summary file name · c6b4115d
  bow authored Jul 28, 2014
  
  c6b4115d
- Output cutadapt statistics correctly in summary files · 556fc8c1
  bow authored Jul 28, 2014
  
  556fc8c1
- Fix on fastqc jobs · cde8f1a6
  Peter van 't Hof authored Jul 28, 2014
  
  cde8f1a6
- Revert "Fix on fastqc jobs" · 373dbb5c
  Peter van 't Hof authored Jul 28, 2014
```
This reverts commit 5945ab1746a433f4c9c2100176934d7ee86c38a2.
```
  373dbb5c
- Fix on fastqc jobs · 613343f7
  Peter van 't Hof authored Jul 28, 2014
  
  613343f7