Commit 9e88effb authored 10 years ago by bow

Merge branch 'feature-fix_missing_values' into 'develop'

Feature fix missing values

Fix for wrong messages when config value does not exist

Now also fix for #112

See merge request !89

parents 1047c24a fbf67f2c

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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala 2 additions, 2 deletions

...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 1 addition, 1 deletion

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 1 addition, 1 deletion

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 6 additions, 6 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 41 additions, 8 deletions

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 3 additions, 3 deletions

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala 4 additions, 4 deletions

...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala 4 additions, 11 deletions

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala 19 additions, 21 deletions

...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala 3 additions, 3 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala 1 addition, 1 deletion

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala 1 addition, 1 deletion

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala 1 addition, 1 deletion

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala 1 addition, 1 deletion

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala 1 addition, 1 deletion

.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala 43 additions, 29 deletions

...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala 0 additions, 3 deletions

...st/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala

with 135 additions and 100 deletions

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