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- biopet-framework/.gitignore 1 addition, 0 deletionsbiopet-framework/.gitignore
- biopet-framework/README 0 additions, 0 deletionsbiopet-framework/README
- biopet-framework/pom.xml 113 additions, 0 deletionsbiopet-framework/pom.xml
- biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala 148 additions, 0 deletions...ework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala
- biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala 34 additions, 0 deletions...work/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
- biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala 71 additions, 0 deletions...src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
- biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala 59 additions, 0 deletions...k/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala
- biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala 71 additions, 0 deletions...k/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala
- biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala 16 additions, 0 deletions...ork/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
- flexiprep/.gitignore 1 addition, 0 deletionsflexiprep/.gitignore
- flexiprep/README 0 additions, 0 deletionsflexiprep/README
- flexiprep/pom.xml 117 additions, 0 deletionsflexiprep/pom.xml
- flexiprep/run_flexiprep.sh 7 additions, 0 deletionsflexiprep/run_flexiprep.sh
- flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqSync.scala 34 additions, 0 deletions...a/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqSync.scala
- flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcToContams.scala 28 additions, 0 deletions...umc/sasc/biopet/pipelines/flexiprep/FastqcToContams.scala
- flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcToQualtype.scala 26 additions, 0 deletions...mc/sasc/biopet/pipelines/flexiprep/FastqcToQualtype.scala
- flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala 173 additions, 0 deletions...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
- gatk/.gitignore 1 addition, 0 deletionsgatk/.gitignore
- gatk/README 0 additions, 0 deletionsgatk/README
- gatk/pom.xml 122 additions, 0 deletionsgatk/pom.xml
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