Commit cbbd03b7 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into Fix-BIOPET-479

parents 1e46be60 0140969c
...@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
} }
}) })
logger.info("Adding report") val writeHtmlReport: Boolean = config("write_html_report", default = true)
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) => if (writeHtmlReport) {
logger.info("Write report is skipped because sample flag is used") logger.info("Adding report")
case _ => reportClass.foreach { report => this match {
for (f <- functions) f match { case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
case w: WriteSummary => report.deps :+= w.jobOutputFile logger.info("Write report is skipped because sample flag is used")
case _ => case _ => reportClass.foreach { report =>
for (f <- functions) f match {
case w: WriteSummary => report.deps :+= w.jobOutputFile
case _ =>
}
report.jobOutputFile = new File(report.outputDir, ".report.out")
add(report)
} }
report.jobOutputFile = new File(report.outputDir, ".report.out")
add(report)
} }
} }
......
...@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference { ...@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var R2: File = _ var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R") @Input(doc = "The reference file for the bam files.", shortName = "R")
var reference: File = null var reference: File = _
@Output(doc = "Output file SAM", shortName = "output") @Output(doc = "Output file SAM", shortName = "output")
var output: File = _ var output: File = _
...@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference { ...@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var k: Option[Int] = config("k") var k: Option[Int] = config("k")
var r: Option[Float] = config("r") var r: Option[Float] = config("r")
var S: Boolean = config("S", default = false) var S: Boolean = config("S", default = false)
var M: Boolean = config("M", default = true) var M: Boolean = config("M", default = false)
var w: Option[Int] = config("w") var w: Option[Int] = config("w")
var d: Option[Int] = config("d") var d: Option[Int] = config("d")
var c: Option[Int] = config("c") var c: Option[Int] = config("c")
...@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference { ...@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if (reference == null) reference = referenceFasta() if (reference == null) reference = referenceFasta()
} }
def cmdLine = { def cmdLine: String = {
required(executable) + required(executable) +
required("mem") + required("mem") +
optional("-k", k) + optional("-k", k) +
......
...@@ -38,6 +38,8 @@ class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFuncti ...@@ -38,6 +38,8 @@ class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFuncti
@Argument(doc = "Samplename") @Argument(doc = "Samplename")
var sampleName: String = _ var sampleName: String = _
override def defaultCoreMemory = 4.0
override def cmdLine = super.cmdLine + override def cmdLine = super.cmdLine +
required("-i", input) + required("-i", input) +
required("-o", output) + required("-o", output) +
......
...@@ -36,11 +36,6 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller { ...@@ -36,11 +36,6 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF")) override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF"))
override def defaults = Map("haplotypecaller" -> Map(
"variant_index_type" -> "LINEAR",
"variant_index_parameter" -> 128000)
)
def biopetScript() { def biopetScript() {
gVcfFiles = for ((sample, inputBam) <- inputBams) yield { gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz")) val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
......
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