From 5421af1141ce7adb245fd392141a4a3a007a2790 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 Oct 2015 20:38:30 +0200
Subject: [PATCH] Use normal pipes instead of fifo pipes
---
.../nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 3 +--
.../biopet/pipelines/bammetrics/scripts/CoverageStats.scala | 4 ++--
.../sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala | 2 +-
3 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 76685a427..ed89542f2 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -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")
}
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
index 212724776..4a4795cf9 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
@@ -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) +
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
index 98024e79e..efb3c1abe 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
@@ -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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