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- bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 2 additions, 1 deletion...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 14 additions, 14 deletions...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 2 additions, 2 deletions...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala 2 additions, 2 deletions...ork/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala 2 additions, 2 deletions.../src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala 2 additions, 2 deletions...lumc/sasc/biopet/function/PythonCommandLineFunction.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala 2 additions, 2 deletions...src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala 2 additions, 2 deletions...rk/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala 2 additions, 2 deletions...cala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala 1 addition, 1 deletion...lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala 1 addition, 1 deletion...umc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala 1 addition, 1 deletion...in/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala 2 additions, 2 deletions...cala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala 1 addition, 1 deletion...lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala 3 additions, 3 deletions...n/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala 5 additions, 5 deletions...ain/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala 3 additions, 3 deletions...ain/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
- mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala 3 additions, 3 deletions...ain/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
- mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala 2 additions, 2 deletions...in/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
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