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- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 33 additions, 0 deletions.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
- public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 2 additions, 3 deletions.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
- public/biopet-extentsions/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-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala 0 additions, 3 deletions...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
- public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala 2 additions, 3 deletions...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
- public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala 0 additions, 3 deletions...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala 1 addition, 2 deletions...in/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala 3 additions, 20 deletions...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala 0 additions, 87 deletions...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala 0 additions, 3 deletions...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala 40 additions, 30 deletions...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala 0 additions, 74 deletions...la/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
- public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala 1 addition, 1 deletion...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
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