Merge branch 'fix-depedencies' into 'develop'
Fix depedencies This will create a json file what will store job and file dependencies at the start of the pipeline. See merge request !269
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- public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala 1 addition, 1 deletion...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 17 additions, 8 deletions...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala 0 additions, 5 deletions...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala 121 additions, 0 deletions...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala 0 additions, 5 deletions...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala 1 addition, 0 deletions...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
- public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala 5 additions, 3 deletions...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala 14 additions, 4 deletions...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
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