Commit 554dbdb0 authored 10 years ago by Sander Bollen

Merge branch 'develop' into feature-toucan

Conflicts:
	public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

parents 334972e7 bd732f66

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public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/pyfastqc/__init__.py 0 additions, 232 deletions

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public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py 16 additions, 0 deletions

...rces/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 15 additions, 0 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 15 additions, 0 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 15 additions, 0 deletions

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 19 additions, 0 deletions

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 15 additions, 0 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala 15 additions, 0 deletions

...ork/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala 15 additions, 0 deletions

...src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 129 additions, 7 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala 15 additions, 0 deletions

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala 19 additions, 4 deletions

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala 133 additions, 44 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala 74 additions, 0 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala 23 additions, 10 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala 92 additions, 8 deletions

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala 15 additions, 0 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala 15 additions, 0 deletions

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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala 12 additions, 3 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 15 additions, 0 deletions

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