diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala index 9a4e43f41d51dcac0bb9fa6d4221f68bcb33dc01..caab2715ee7d859f809adcbf770b52e24818783e 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala @@ -46,6 +46,8 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools { if (input.getName.endsWith(".bam")) inputTag = "-abam" } + override val defaultVmem = "6G" + /** Returns command to execute */ def cmdLine = required(executable) + required("coverage") + required(inputTag, input) +