Commit 490fb781 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into fix-BIOPET-655

parents 58a402b7 4fb8a7b6
......@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
})
logger.info("Adding report")
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write report is skipped because sample flag is used")
case _ => reportClass.foreach { report =>
for (f <- functions) f match {
case w: WriteSummary => report.deps :+= w.jobOutputFile
case _ =>
val writeHtmlReport: Boolean = config("write_html_report", default = true)
if (writeHtmlReport) {
logger.info("Adding report")
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write report is skipped because sample flag is used")
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)
}
}
......
......@@ -56,12 +56,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
if (outputName == null) {
if (fastqR1.nonEmpty) outputName = fastqR1.headOption.map(_.getName
.stripSuffix(".gz")
.stripSuffix(".fastq")
.stripSuffix(".fq"))
.getOrElse("noName")
else outputName = bamFile.map(_.getName.stripSuffix(".bam")).getOrElse("noName")
outputName = sampleId.getOrElse("noName") + libId.map("-" + _).getOrElse("")
}
if (fastqR1.nonEmpty) {
......
......@@ -108,7 +108,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears.outputName shouldBe "test"
} else {
// in the following cases the filename should have been determined by the filename
gears.outputName shouldBe (if (inputMode == Some("bam")) "bamfile" else "R1")
gears.outputName shouldBe "sampleName-libName"
}
val pipesJobs = gears.functions.filter(_.isInstanceOf[BiopetCommandLineFunction])
......
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