Commits · 1dd927a380a5915cf6f083f7b1ab9bd991ef287b · Mirrors / biopet.biopet

Sep 22, 2015
- Merge remote-tracking branch 'origin/develop' into feature-pipeable · 1dd927a3
  Peter van 't Hof authored 9 years ago
  
  1dd927a3
- 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
- Merge branch 'feature-input_files_checking' into develop · f4063de9
  Sander Bollen authored 9 years ago
  
  Conflicts: public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
  f4063de9
- Merge branch 'fix-remove_temp_files' into 'develop' · 92170802
  Sander Bollen authored 9 years ago
  
  Fix remove temp files I did see a lot of temp files that where not removed after testing. This will remove all temp files on exit of a tool / test. See merge request !238
  92170802
- Merge branch 'fix-sample_flag_summary_report' into 'develop' · bcd97f00
  Sander Bollen authored 9 years ago
  
  Fix summary when --sample flag is used in multisample pipelines Fixes #206 See merge request !237
  bcd97f00
- This will remove tempfiles on exit · 2fdf69e7
  Peter van 't Hof authored 9 years ago
  
  2fdf69e7
- Merge branch 'feature-gatk_et_option' into 'develop' · 6300d051
  Sander Bollen authored 9 years ago
  
  Add et option to gatk jobs Added the et option to gatk. @a.h.b.bollen: could you maybe test this? I don't have a key See merge request !169
  6300d051
- 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
- Merge branch 'fix-report' into 'develop' · d5ae90cf
  Sander Bollen authored 9 years ago
  
  Fix report Fixes #202 See merge request !236
  d5ae90cf
- Merge branch 'feature-external_examples' into 'develop' · f65704c6
  Sander Bollen authored 9 years ago
  
  Feature external examples Added some examples how to make a pipeline and maven artefact that will use biopet, like Magpie 2.0. Added this as part of #134 See merge request !227
  f65704c6
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
- Fix protected package · 253f3d6a
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit a715d472)
  253f3d6a
- 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
- skip canRead when file does not exist · 5d8fb79d
  Peter van 't Hof authored 9 years ago
  
  5d8fb79d
- Fastq sync is not intermediate · 5f7b2cbe
  Peter van 't Hof authored 9 years ago
  
  5f7b2cbe
- Disable default toucan · 76488b88
  Peter van 't Hof authored 9 years ago
  
  76488b88
- Adding input files to check · 3c83721a
  Peter van 't Hof authored 9 years ago
  
  3c83721a
- Fix protected package · 37b9a6d3
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit a715d472)
  37b9a6d3
- Fix protected package · a715d472
  Peter van 't Hof authored 9 years ago
  
  a715d472
- Fix error cache · 5035e251
  Peter van 't Hof authored 9 years ago
  
  5035e251
- Code style fix · d953a079
  Peter van 't Hof authored 9 years ago
  
  d953a079
- Sync with develop and fix build issues · c1f9f9e8
  Peter van 't Hof authored 9 years ago
  
  c1f9f9e8
- Fix imports · 4e12b4c4
  Peter van 't Hof authored 9 years ago
  
  4e12b4c4
Sep 17, 2015

Fixed qc stats in report · ac12d5a9
Peter van 't Hof authored 9 years ago

ac12d5a9
Rename header · b248300c
Peter van 't Hof authored 9 years ago

b248300c
Fix plots for library level · c7b0392c
Peter van 't Hof authored 9 years ago

c7b0392c
Fix sample bamMetrics · 2d950663
Peter van 't Hof authored 9 years ago

2d950663
Fix LinePlot · 334a0969
Peter van 't Hof authored 9 years ago

334a0969
Merge remote-tracking branch 'origin/develop' into feature-input_files_checking · 631dae57
Peter van 't Hof authored 9 years ago
```
Conflicts:
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
```
631dae57
Switch example to BiopetCore · 36b53286
Peter van 't Hof authored 9 years ago

36b53286
Merge remote-tracking branch 'origin/develop' into feature-external_examples · 90f25629
Peter van 't Hof authored 9 years ago

90f25629

Merge remote-tracking branch 'origin/develop' into feature-pipeable · b230161f

Conflicts:
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala

b230161f