Commit 5421af11 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Use normal pipes instead of fifo pipes

parent 1020c2d1
......@@ -176,8 +176,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val covStats = CoverageStats(this, coverageFile, targetDir)
covStats.title = Some("Coverage for " + targetName)
covStats.subTitle = Some(".")
val pipe = new BiopetFifoPipe(this, bedCov :: covStats :: Nil)
add(pipe)
add(bedCov | covStats)
addSummarizable(covStats, targetName + "_cov_stats")
}
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class CoverageStats(val root: Configurable) extends PythonCommandLineFunction with Summarizable {
setPythonScript("bedtools_cov_stats.py")
@Input(doc = "Input file")
@Input(doc = "Input file", required = false)
var input: File = _
@Output(doc = "output File")
......@@ -41,7 +41,7 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction wi
override def defaultCoreMemory = 9.0
def cmdLine = getPythonCommand +
required(input) +
(if (inputAsStdin) " - " else required(input)) +
required("--plot", plot) +
optional("--title", title) +
optional("--subtitle", subTitle) +
......
......@@ -56,7 +56,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
conditional(depth, "-d") +
conditional(sameStrand, "-s") +
conditional(diffStrand, "-S") +
" > " + required(output)
(if (outputAsStsout) "" else " > " + required(output))
}
object BedtoolsCoverage {
......
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