Commit f3dc2736 authored 8 years ago by Peter van 't Hof Committed by GitHub 8 years ago

Merge pull request #9 from biopet/bios-slurm

Udate Bios branch to latest develop (with SLurm support)

parents 86e77e81 251846cb

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.gitmodules 3 additions, 0 deletions

.gitmodules
Jenkinsfile 39 additions, 0 deletions

Jenkinsfile
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala 0 additions, 2 deletions

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp 4 additions, 4 deletions

...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp 2 additions, 2 deletions

...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp 102 additions, 0 deletions

...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp 3 additions, 3 deletions

...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp 102 additions, 0 deletions

.../lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 24 additions, 12 deletions

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala 144 additions, 203 deletions

...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala 4 additions, 3 deletions

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala 2 additions, 1 deletion

...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 11 additions, 4 deletions

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 78 additions, 6 deletions

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala 15 additions, 3 deletions

...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 14 additions, 4 deletions

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala 9 additions, 9 deletions

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala 270 additions, 0 deletions

.../main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala 41 additions, 5 deletions

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala 148 additions, 0 deletions

...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

with 1015 additions and 261 deletions

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