Merge commit 'cfae9015'
Conflicts: flexiprep/nbactions.xml gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala mapping/examples/test.json mapping/nbactions.xml pom.xml
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- bam-metrics/.gitignore 0 additions, 1 deletionbam-metrics/.gitignore
- bam-metrics/nbactions.xml 0 additions, 49 deletionsbam-metrics/nbactions.xml
- bam-metrics/pom.xml 0 additions, 140 deletionsbam-metrics/pom.xml
- biopet-framework/examples/bam-metrics.json 0 additions, 0 deletionsbiopet-framework/examples/bam-metrics.json
- biopet-framework/examples/flexiprep.json 0 additions, 0 deletionsbiopet-framework/examples/flexiprep.json
- biopet-framework/examples/gatk-benchmark-genotyping.json 0 additions, 0 deletionsbiopet-framework/examples/gatk-benchmark-genotyping.json
- biopet-framework/examples/gatk-genotypeing.json 0 additions, 0 deletionsbiopet-framework/examples/gatk-genotypeing.json
- biopet-framework/examples/gatk-pipeline.json 0 additions, 0 deletionsbiopet-framework/examples/gatk-pipeline.json
- biopet-framework/examples/gatk-variantcalling.json 0 additions, 0 deletionsbiopet-framework/examples/gatk-variantcalling.json
- biopet-framework/examples/gatk-vcf-sample-compare.json 0 additions, 0 deletionsbiopet-framework/examples/gatk-vcf-sample-compare.json
- biopet-framework/examples/mapping.json 0 additions, 1 deletionbiopet-framework/examples/mapping.json
- biopet-framework/pom.xml 53 additions, 85 deletionsbiopet-framework/pom.xml
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 47 additions, 0 deletions...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala 0 additions, 0 deletions...n/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala 0 additions, 0 deletions.../scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala 0 additions, 0 deletions...cala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 0 additions, 0 deletions...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala 0 additions, 0 deletions...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala 0 additions, 0 deletions...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala 0 additions, 0 deletions...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
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