Commit c1acac57 authored 9 years ago by Peter van 't Hof

Merge remote-tracking branch 'remotes/origin/develop' into fix-warns

Conflicts:
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

parents c7847542 29a61dfe

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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala 4 additions, 3 deletions

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp 5 additions, 1 deletion

...lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 5 additions, 5 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 1 addition, 1 deletion

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala 25 additions, 10 deletions

...k/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala 1 addition, 1 deletion

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 4 additions, 4 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala 4 additions, 4 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala 2 additions, 2 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 1 addition, 1 deletion

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 2 additions, 2 deletions

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

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

...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala 1 addition, 1 deletion

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala 1 addition, 1 deletion

...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala 2 additions, 2 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala 2 additions, 2 deletions

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala 4 additions, 4 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

with 70 additions and 50 deletions

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