Commits · 273e70f5bac94ff8f9ab37624ab02cf1ab661d30 · Mirrors / biopet.biopet

17 Feb, 2015 1 commit
- Converted fastqc to new summary · 273e70f5
  Peter van 't Hof authored Feb 17, 2015
  
  273e70f5
16 Feb, 2015 1 commit
- Added summary framework to mapping and flexiprep · 0c3deab9
  Peter van 't Hof authored Feb 16, 2015
  
  0c3deab9
14 Feb, 2015 1 commit
- Added init version of summary · e8f474c1
  Peter van 't Hof authored Feb 14, 2015
  
  e8f474c1
12 Feb, 2015 1 commit
- Change outputDir to File · 8ca365cb
  Peter van 't Hof authored Feb 12, 2015
  
  8ca365cb
06 Feb, 2015 1 commit
- Fix NullPointerException caused by Option[File] being null · c78ca1be
  bow authored Feb 06, 2015
  
  c78ca1be
03 Feb, 2015 4 commits
- Change to option types · 71eb5183
  Peter van 't Hof authored Feb 03, 2015
  
  71eb5183
- Use requirements check on mapping and flexiprep pipeline · a9c9dfbd
  bow authored Feb 03, 2015
  
  a9c9dfbd
- Rename libraryId -> libId for consistency · ad0c55bc
  bow authored Feb 03, 2015
  
  ad0c55bc
- Expose Flexiprep sampleId and libraryId back to the command line · daf3d591
  bow authored Feb 03, 2015
  
  daf3d591
29 Jan, 2015 2 commits
- Remove unused import · 131f4a6f
  bow authored Jan 29, 2015
  
  131f4a6f
- Use sync tool and update its wrapper · 96d44ee9
  bow authored Jan 29, 2015
  
  96d44ee9
28 Jan, 2015 1 commit
- Renaming values · bbd005c3
  Peter van 't Hof authored Jan 28, 2015
  
  bbd005c3
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 1 commit
- Wrappers are now split in general and specific flexiprep extensions · 6b5c4320
  Peter van 't Hof authored Jul 30, 2014
  
  6b5c4320