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Added BiopetCommandlineFunction
All commandlinefunctions now extends from this trait
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- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 116 additions, 0 deletions.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala 30 additions, 0 deletions...lumc/sasc/biopet/function/PythonCommandLineFunction.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala 8 additions, 9 deletions...src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala 9 additions, 9 deletions...rk/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala 21 additions, 36 deletions...n/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala 25 additions, 50 deletions...ain/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala 38 additions, 45 deletions...ain/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala 5 additions, 11 deletions...c/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala 6 additions, 12 deletions.../biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala 5 additions, 11 deletions...biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala 5 additions, 12 deletions...umc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
- flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala 5 additions, 12 deletions...c/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
- mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala 22 additions, 39 deletions...ain/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
- mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala 50 additions, 29 deletions...in/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
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