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
Showing
- 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
bam-metrics/.gitignore
deleted
100644 → 0
bam-metrics/nbactions.xml
deleted
100644 → 0
bam-metrics/pom.xml
deleted
100644 → 0
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
File moved
Please register or sign in to comment