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 f6a6dc090defdb238f76b68f21189faf38fd207c..981417a012d7d3e17ec87ad879e622d77273b01f 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
@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
@@ -151,33 +151,24 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val targetDir = new File(outputDir, targetName)
val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
- output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam"),
+ output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
minOverlap = config("strict_intersect_overlap", default = 1.0))
- biStrict.isIntermediate = true
- add(biStrict)
- add(SamtoolsFlagstat(this, biStrict.output, targetDir))
val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
- add(biopetFlagstatStrict)
addSummarizable(biopetFlagstatStrict, targetName + "_biopet_flagstat_strict")
+ add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
- output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam"),
+ output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
minOverlap = config("loose_intersect_overlap", default = 0.01))
- biLoose.isIntermediate = true
- add(biLoose)
- add(SamtoolsFlagstat(this, biLoose.output, targetDir))
val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
- add(biopetFlagstatLoose)
addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
+ add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
- val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
-
- //FIXME:should use piping
- add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), isIntermediate = true)
- val covStats = CoverageStats(this, coverageFile, targetDir)
- covStats.title = Some("Coverage for " + targetName)
- covStats.subTitle = Some(".")
- add(covStats)
+ val bedCov = BedtoolsCoverage(this, intervals.bed, inputBam, depth = true)
+ val covStats = CoverageStats(this, targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
+ covStats.title = Some("Coverage Plot")
+ covStats.subTitle = Some(s"for file '$targetName.bed'")
+ 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 212724776c3dad98a1c514d17d6c66623c169127..a12aced89381468c3e51bdb6dc533af08446eb45 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) +
@@ -55,11 +55,10 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction wi
}
object CoverageStats {
- def apply(root: Configurable, input: File, outputDir: File): CoverageStats = {
+ def apply(root: Configurable, outputDir: File, name: String): CoverageStats = {
val coverageStats = new CoverageStats(root)
- coverageStats.input = input
- coverageStats.output = new File(outputDir, input.getName + ".stats")
- coverageStats.plot = new File(outputDir, input.getName + ".stats.png")
+ coverageStats.output = new File(outputDir, name + ".stats")
+ coverageStats.plot = new File(outputDir, name + ".stats.png")
coverageStats
}
}
diff --git a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
index 33304cb198807f46d3801ddfc9b05eaa7d555fe4..dcd32fe1d71924353daea489b623745b729b72fd 100644
--- a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+++ b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
@@ -81,12 +81,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)
- bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe (1 + (regions * 2))
- bammetrics.functions.count(_.isInstanceOf[SamtoolsFlagstat]) shouldBe (1 + (regions * 2))
- bammetrics.functions.count(_.isInstanceOf[BedtoolsIntersect]) shouldBe (regions * 2)
-
- bammetrics.functions.count(_.isInstanceOf[BedtoolsCoverage]) shouldBe regions
- bammetrics.functions.count(_.isInstanceOf[CoverageStats]) shouldBe regions
+ bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe 1
}
// remove temporary run directory all tests in the class have been run
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 98024e79e25aa0c98624e2ff0e01783d37e35537..85cd80712d496259ad043c6fe851640b800d193f 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
@@ -41,32 +41,26 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
@Argument(doc = "diffStrand", required = false)
var diffStrand: Boolean = false
- var inputTag = "-a"
-
- override def beforeCmd() {
- if (input.getName.endsWith(".bam")) inputTag = "-abam"
- }
-
override def defaultCoreMemory = 4.0
/** Returns command to execute */
def cmdLine = required(executable) + required("coverage") +
- required(inputTag, input) +
+ required("-a", input) +
required("-b", intersectFile) +
conditional(depth, "-d") +
conditional(sameStrand, "-s") +
conditional(diffStrand, "-S") +
- " > " + required(output)
+ (if (outputAsStsout) "" else " > " + required(output))
}
object BedtoolsCoverage {
/** Returns defaul bedtools coverage */
- def apply(root: Configurable, input: File, intersect: File, output: File,
- depth: Boolean = true, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
+ def apply(root: Configurable, input: File, intersect: File, output: Option[File] = None,
+ depth: Boolean = false, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
val bedtoolsCoverage = new BedtoolsCoverage(root)
bedtoolsCoverage.input = input
bedtoolsCoverage.intersectFile = intersect
- bedtoolsCoverage.output = output
+ output.foreach(bedtoolsCoverage.output = _)
bedtoolsCoverage.depth = depth
bedtoolsCoverage.sameStrand = sameStrand
bedtoolsCoverage.diffStrand = diffStrand
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
index 75f179ad326939d65f01031a4e909c59565e4906..bbd110c88d4d45a516fb8df3c92ff35c7b961284 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
@@ -40,6 +40,8 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
var inputTag = "-a"
+ var ubam = false
+
override def beforeCmd() {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
@@ -50,6 +52,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
required("-b", intersectFile) +
optional("-f", minOverlap) +
conditional(count, "-c") +
+ conditional(ubam, "-ubam") +
" > " + required(output)
}
@@ -61,6 +64,7 @@ object BedtoolsIntersect {
bedtoolsIntersect.input = input
bedtoolsIntersect.intersectFile = intersect
bedtoolsIntersect.output = output
+ if (output.getName.endsWith(".sam")) bedtoolsIntersect.ubam = true
bedtoolsIntersect.minOverlap = minOverlap
bedtoolsIntersect.count = count
bedtoolsIntersect
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index c8b81c0c4d31d6424db74390390c758096478838..cbe6fd6eb56e9d7eab647cad238456717d10a6b8 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -173,19 +173,22 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: File) {
- val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.sense.coverage"),
+ val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed,
+ output = Some(new File(outputDir, outputPrefix + ".genome.sense.coverage")),
depth = false, sameStrand = true, diffStrand = false)
val countSense = new BedtoolsCoverageToCounts(this)
countSense.input = bedtoolsSense.output
countSense.output = new File(outputDir, outputPrefix + ".genome.sense.counts")
- val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.antisense.coverage"),
+ val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed,
+ output = Some(new File(outputDir, outputPrefix + ".genome.antisense.coverage")),
depth = false, sameStrand = false, diffStrand = true)
val countAntisense = new BedtoolsCoverageToCounts(this)
countAntisense.input = bedtoolsAntisense.output
countAntisense.output = new File(outputDir, outputPrefix + ".genome.antisense.counts")
- val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.coverage"),
+ val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed,
+ output = Some(new File(outputDir, outputPrefix + ".genome.coverage")),
depth = false, sameStrand = false, diffStrand = false)
val count = new BedtoolsCoverageToCounts(this)
count.input = bedtools.output
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 5e80f114c82bd16fb1efd7788158f31d1c2c0f05..b628744d325184b46b176c1b9b9871208b72a170 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -246,7 +246,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
}).toList)
lazy val variantcalling = if (config("single_sample_variantcalling", default = false).asBoolean) {
- Some(makeVariantcalling(multisample = true))
+ Some(makeVariantcalling(multisample = false))
} else None
/** This will add sample jobs */