diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index 767b655e4156a0f94f304391dde4fe66471b07eb..1d015a49c3b467cb129c6e059ef572c0162ecb3d 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
@@ -87,6 +87,12 @@ class ShivaTest extends TestNGSuite with Matchers {
object ShivaTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
@@ -130,8 +136,8 @@ object ShivaTest {
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "1_1_R1.fq",
- "R2" -> "1_1_R2.fq"
+ "R1" -> inputTouch("1_1_R1.fq"),
+ "R2" -> inputTouch("1_1_R2.fq")
)
)
)))
@@ -139,12 +145,12 @@ object ShivaTest {
val sample2 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "3_1_R1.fq",
- "R2" -> "3_1_R2.fq"
+ "R1" -> inputTouch("2_1_R1.fq"),
+ "R2" -> inputTouch("2_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> "3_2_R1.fq",
- "R2" -> "3_2_R2.fq"
+ "R1" -> inputTouch("2_2_R1.fq"),
+ "R2" -> inputTouch("2_2_R2.fq")
)
)
)))
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
index 2c60207a82fae9da823eb02d7a860b5dd8be1834..8e8a1eddf9e5d6b5aab36c4c6fea7d35ea2da82e 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
@@ -73,7 +73,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
- pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+ pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
val illegalArgumentException = pipeline.inputBams.isEmpty ||
(!raw && !bcftools &&
@@ -107,6 +107,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): File = {
+ val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+ Files.touch(file)
+ file
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index 451350227e5620ae612212eb341e0acae49ad958..fb9e39611fd861f9158503581f17d4bd12e6cb30 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -35,6 +35,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
var bamFile: File = null
def init(): Unit = {
+ inputFiles :+= new InputFile(bamFile)
}
def biopetScript(): Unit = {
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 defb8361c68974ccffdddcba26dbe7700d58fea2..f6a6dc090defdb238f76b68f21189faf38fd207c 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
@@ -71,7 +71,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
}
/** executed before script */
- def init() {
+ def init(): Unit = {
+ inputFiles :+= new InputFile(inputBam)
}
/** Script to add jobs */
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 7e97b4a78e1176b1603a7ae5aec10057c4bd0175..33304cb198807f46d3801ddfc9b05eaa7d555fe4 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
@@ -69,7 +69,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
val bammetrics: BamMetrics = initPipeline(map)
- bammetrics.inputBam = new File("input.bam")
+ bammetrics.inputBam = BamMetricsTest.bam
bammetrics.sampleId = Some("1")
bammetrics.libId = Some("1")
bammetrics.script()
@@ -98,6 +98,10 @@ class BamMetricsTest extends TestNGSuite with Matchers {
object BamMetricsTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+
+ val bam = new File(outputDir, "input" + File.separator + "bla.bam")
+ Files.touch(bam)
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
index 1990085cef63fc60c637e04bb17811a20b837f85..a2a1f832843072d5abc9d46fb0280ba3b2c19ea4 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+++ b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
@@ -89,6 +89,8 @@ trait BastyTrait extends MultiSampleQScript {
addAll(shiva.functions)
addSummaryQScript(shiva)
+ inputFiles :::= shiva.inputFiles
+
addSamplesJobs()
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index f35c07a0a4497fa4a36e0b34a1b640cf8f03364c..fa714c9423707456f1f6d1cfa6f2617c44318218 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -48,6 +48,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
var outputFiles: Map[String, File] = Map()
+ type InputFile = BiopetQScript.InputFile
+
+ var inputFiles: List[InputFile] = Nil
+
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
var qSettings: QSettings
@@ -86,7 +90,16 @@ trait BiopetQScript extends Configurable with GatkLogging {
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
- reportClass.foreach(add(_))
+ inputFiles.foreach { i =>
+ if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
+ else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
+ }
+
+ 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(add(_))
+ }
Logging.checkErrors()
}
@@ -103,3 +116,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
add(function)
}
}
+
+object BiopetQScript {
+ protected case class InputFile(file: File, md5: Option[String] = None)
+}
\ No newline at end of file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index d8756c7b91cd27b330b4697aab0d94c9f436c98a..17631709f12db8a3e3b25253afc49fadd3820e32 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -26,7 +26,7 @@ trait MultiSampleQScript extends SummaryQScript {
qscript =>
@Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
- private val onlySamples: List[String] = Nil
+ private[core] val onlySamples: List[String] = Nil
require(globalConfig.map.contains("samples"), "No Samples found in config")
@@ -131,7 +131,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
- if (onlySamples.isEmpty) {
+ if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
addMultiSampleJobs()
} else onlySamples.foreach(sampleId => samples.get(sampleId) match {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
new file mode 100644
index 0000000000000000000000000000000000000000..0ae2587f7928bb8d8cfe3e157f79fec7afff031a
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
@@ -0,0 +1,40 @@
+package nl.lumc.sasc.biopet.core.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.WriteSummary
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
+
+/**
+ * This class checks md5sums and give an exit code 1 when md5sum is not the same
+ *
+ * Created by pjvanthof on 16/08/15.
+ */
+class CheckChecksum extends InProcessFunction {
+ @Input(required = true)
+ var inputFile: File = _
+
+ @Input(required = true)
+ var checksumFile: File = _
+
+ @Argument(required = true)
+ var checksum: String = _
+
+ override def freezeFieldValues(): Unit = {
+ super.freezeFieldValues()
+ jobOutputFile = new File(checksumFile.getParentFile, checksumFile.getName + ".check.out")
+ }
+
+ /** Exits whenever the input md5sum is not the same as the output md5sum */
+ def run: Unit = {
+ val outputChecksum = WriteSummary.parseChecksum(checksumFile).toLowerCase
+
+ if (outputChecksum != checksum.toLowerCase) {
+ logger.error(s"Input file: '$inputFile' md5sum is not as expected, aborting pipeline")
+
+ // 130 Simulates a ctr-C
+ Runtime.getRuntime.halt(130)
+ }
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index 6c1bc388153f37d746cbf8a173a5ecc85c7201d5..344a6139c88340fe96b6ef92bc49f9d5637615f1 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -231,6 +231,7 @@ object ReportBuilder {
case Some(template) => template
case _ =>
val tempFile = File.createTempFile("ssp-template", new File(location).getName)
+ tempFile.deleteOnExit()
IoUtils.copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
templateCache += location -> tempFile
tempFile
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index 52c77fe8a63a090f2c4bb776da39647f9a35379e..6eaae5391f4712b427cc0307d7a480d1aee1e712 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.extensions.Md5sum
+import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
import scala.collection.mutable
@@ -27,7 +27,7 @@ import scala.collection.mutable
*
* Created by pjvan_thof on 2/14/15.
*/
-trait SummaryQScript extends BiopetQScript {
+trait SummaryQScript extends BiopetQScript { qscript =>
/** Key is sample/library, None is sample or library is not applicable */
private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
@@ -116,6 +116,20 @@ trait SummaryQScript extends BiopetQScript {
//TODO: add more checksums types
}
+ for (inputFile <- inputFiles) {
+ inputFile.md5 match {
+ case Some(checksum) => {
+ val checkMd5 = new CheckChecksum
+ checkMd5.inputFile = inputFile.file
+ require(SummaryQScript.md5sumCache.contains(inputFile.file), "Md5 job is not executed, checksum file can't be found")
+ checkMd5.checksumFile = SummaryQScript.md5sumCache(inputFile.file)
+ checkMd5.checksum = checksum
+ add(checkMd5)
+ }
+ case _ =>
+ }
+ }
+
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList) {
summarizable match {
case f: BiopetCommandLineFunctionTrait => f.beforeGraph()
@@ -135,7 +149,11 @@ trait SummaryQScript extends BiopetQScript {
for ((_, file) <- this.summaryFiles)
addChecksum(file)
- add(writeSummary)
+ this match {
+ case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+ logger.info("Write summary is skipped because sample flag is used")
+ case _ => add(writeSummary)
+ }
}
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 3db4607d6288f84b204033ee3db186ee76771935..3530e4d0ad05f1916ccf344e625bbe5b097c0f65 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -153,10 +153,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
def parseFile(file: File): Map[String, Any] = {
val map: mutable.Map[String, Any] = mutable.Map()
map += "path" -> file.getAbsolutePath
- if (md5sum) map += "md5" -> parseChecksum(SummaryQScript.md5sumCache(file))
+ if (md5sum) map += "md5" -> WriteSummary.parseChecksum(SummaryQScript.md5sumCache(file))
map.toMap
}
-
+}
+object WriteSummary {
/** Retrive checksum from file */
def parseChecksum(checksumFile: File): String = {
Source.fromFile(checksumFile).getLines().toList.head.split(" ")(0)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index 5a3e1e3f26588c103a4bf5e0a190aa223d064450..e5ba10717a5e32b3baf4dbe059d64dccfdcdcc61 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -57,7 +57,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
override def beforeCmd(): Unit = {
- if (sample == null && inputBam.exists()) {
+ if (sample == null && inputBam.exists() && inputBam.length() > 0) {
val inputSam = SamReaderFactory.makeDefault.open(inputBam)
val readGroups = inputSam.getFileHeader.getReadGroups
val samples = readGroups.map(readGroup => readGroup.getSample).distinct
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index 960c4921debd6e58f45fa00bbb9dc0864dd11c60..62b04375f630ab59fea18d9c1d974bdf038cb767 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -625,6 +625,7 @@ object VcfStats extends ToolCommand {
def executeRscript(resource: String, args: Array[String]): Unit = {
val is = getClass.getResourceAsStream(resource)
val file = File.createTempFile("script.", "." + resource)
+ file.deleteOnExit()
val os = new FileOutputStream(file)
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
index ebe393bfab7bdb8fedec024319e99a5b0ec29a07..d9d8c1bee6bf96bcc98a372585b5a89454775e08 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -31,6 +31,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test def testMainVcf = {
val tmp = File.createTempFile("basty_out", ".fa")
+ tmp.deleteOnExit()
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
@@ -40,6 +41,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test def testMainVcfAndBam = {
val tmp = File.createTempFile("basty_out", ".fa")
+ tmp.deleteOnExit()
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
@@ -49,6 +51,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test def testMainVcfAndBamMore = {
val tmp = File.createTempFile("basty_out", ".fa")
+ tmp.deleteOnExit()
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
index 758cb6be6d6aa0a75c2ec1830e0fa3334beb7626..d919fe400154683f5fef7a061ce76c60aab5f5e7 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
@@ -56,6 +56,7 @@ class BiopetFlagstatTest extends TestNGSuite with MockitoSugar with Matchers {
def testMain() = {
//TODO: Test output file
val output = File.createTempFile("testMain", ".biopetflagstat")
+ output.deleteOnExit()
main(Array("-I", bam.getAbsolutePath, "-o", output.toString))
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
index ffa8be0bcb6c2cf15bf0ad00efeeb54e903eb3df..dd66b204fab38a4fd26fb011ffe6739faf304009 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
@@ -23,7 +23,7 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
-
+ temp.deleteOnExit()
val args = Array("-I", fq, "-o", temp.getAbsolutePath)
main(args)
}
@@ -31,6 +31,7 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testManyOutMain() = {
val files = (0 until 10).map(_ => File.createTempFile("out", ".fastq"))
+ files.foreach(_.deleteOnExit())
var args = Array("-I", fq)
files.foreach(x => args ++= Array("-o", x.getAbsolutePath))
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
index b6de2f8bcca896e8979c2e21fc5bb8651524610a..907270b8c31f3eb152766f03a612101f754ba6c9 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
@@ -29,6 +29,7 @@ class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers
def testMain() = {
val outputFile = File.createTempFile("repeats", ".tsv")
+ outputFile.deleteOnExit()
val args = Array("-I", bam, "-b", bed, "-o", outputFile.toString)
main(args)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
index 032f9a913373c0f3be617e45cc26a928ca69821d..e708bc654b3c81699dcab85bfc07a7e21cd3ea94 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
@@ -28,6 +28,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val tmp = File.createTempFile("mpileup", ".vcf")
+ tmp.deleteOnExit()
val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath)
main(args)
@@ -36,6 +37,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def validateOutVcf() = {
val tmp = File.createTempFile("mpileup", ".vcf")
+ tmp.deleteOnExit()
val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
main(args)
@@ -51,6 +53,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def extraValidateOutVcf() = {
val tmp = File.createTempFile("mpileup", ".vcf")
+ tmp.deleteOnExit()
val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
index 41db9e3ae268a62860fd3fbe9a27e4430165429e..611557d836636aebc71f90e70707035033df6b97 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
@@ -26,6 +26,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
+ temp.deleteOnExit()
val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
main(args)
@@ -34,6 +35,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testOutput() = {
val temp = File.createTempFile("out", ".fastq")
+ temp.deleteOnExit()
val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
index 15d3074c95313c6f2a084c41b4d0a4787bdedddb..5c7731c6dd2ec60b7c8cd01f84c6929026d7e007 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
@@ -22,6 +22,7 @@ class SageCountFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
+ temp.deleteOnExit()
val args = Array("-I", fq, "-o", temp.getAbsolutePath)
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
index 48038ea6f476fd89a945f53cf3d3608661fbcc9c..c86c1ba5a9787c0cdcce00293309500d6f6e4b86 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
@@ -29,9 +29,13 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
val input = resourcePath("/mini.transcriptome.fa")
val output = File.createTempFile("sageCreateLibrary", ".tsv")
+ output.deleteOnExit()
val noTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ noTagsOutput.deleteOnExit()
val antiTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ antiTagsOutput.deleteOnExit()
val allGenesOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ allGenesOutput.deleteOnExit()
val args = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
"--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath, "--noAntiTagsOutput",
@@ -52,9 +56,13 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
def testOutPut = {
val input = resourcePath("/mini.transcriptome.fa")
val output = File.createTempFile("sageCreateLibrary", ".tsv")
+ output.deleteOnExit()
val noTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ noTagsOutput.deleteOnExit()
val antiTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ antiTagsOutput.deleteOnExit()
val allGenesOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ allGenesOutput.deleteOnExit()
val args = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
"--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath, "--noAntiTagsOutput",
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
index b47c507856ec251878057a3823d47d57160045e9..ecd1dae87d5c43a88e722cbb12f7eb18ece3a9b8 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
@@ -26,9 +26,13 @@ class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matcher
val tagLib = resourcePath("/sageTest.tsv")
val sense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ sense.deleteOnExit()
val allSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allSense.deleteOnExit()
val antiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ antiSense.deleteOnExit()
val allAntiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allAntiSense.deleteOnExit()
noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib,
"--countSense", sense.getAbsolutePath, "--countAllSense", allSense.getAbsolutePath,
@@ -50,9 +54,13 @@ class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matcher
val tagLib = resourcePath("/sageTest.tsv")
val sense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ sense.deleteOnExit()
val allSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allSense.deleteOnExit()
val antiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ antiSense.deleteOnExit()
val allAntiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allAntiSense.deleteOnExit()
main(Array("-I", input, "--tagLib", tagLib, "--countSense", sense.getAbsolutePath,
"--countAllSense", allSense.getAbsolutePath, "--countAntiSense", antiSense.getAbsolutePath,
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
index 9866ad47a8efbfad5f34868b82fe415f6e6b8c28..e8a09a9d7cb9af569f2084c95a1b6c2e7f1e1aad 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
@@ -21,6 +21,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testCorrectSampleTsv = {
val tsv = resourcePath("/sample.tsv")
val output = File.createTempFile("testCorrectSampleTsv", ".json")
+ output.deleteOnExit()
noException should be thrownBy main(Array("-i", tsv, "-o", output.toString))
}
@@ -29,6 +30,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testNoSampleColumn() = {
val tsv = resourcePath("/no_sample.tsv")
val output = File.createTempFile("testNoSampleColumn", ".json")
+ output.deleteOnExit()
val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
thrown.getMessage should equal("Sample column does not exist in: " + tsv)
}
@@ -37,6 +39,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testNumberInLibs = {
val tsv = resourcePath("/number.tsv")
val output = File.createTempFile("testNumberInLibs", ".json")
+ output.deleteOnExit()
val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
thrown.getMessage should equal("Sample or library may not start with a number")
}
@@ -45,6 +48,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testSampleIDs = {
val tsv = resourcePath("/same.tsv")
val output = File.createTempFile("testSampleIDs", ".json")
+ output.deleteOnExit()
val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
thrown.getMessage should equal("Combination of Sample_ID_1 and Lib_ID_1 is found multiple times")
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
index 6071fceaaed85a943a4f973ac713d24e8b708952..4f921affbc090031b83c0ee5fea3c64b9c9bdf4c 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -24,6 +24,7 @@ class SummaryToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
def testMain = {
val tsv = resourcePath("/test.summary.json")
val output = File.createTempFile("main", "tsv")
+ output.deleteOnExit()
noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
"-m", "root", "-o", output.toString))
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index af8ff6267d5c73dad9eaa10762b1d356a2641626..a6a70881012480a8e92b9aac1c689e4456f9f8c7 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -47,50 +47,57 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testOutputTypeVcf() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
+ tmpFile.deleteOnExit()
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf.gz").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf.gz")
+ tmpFile.deleteOnExit()
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputTypeBcf() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".bcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".bcf")
+ tmpFile.deleteOnExit()
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputFieldException = {
- val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:AC")
+ val tmpFile = File.createTempFile("VCFWithVCf", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:AC")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Field 'AC' already exists in input vcf")
}
@Test def testInputFieldException = {
- val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpPath, "-f", "CSQ:NEW_CSQ")
+ val tmpFile = File.createTempFile("VCFWithVCf", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:NEW_CSQ")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Field 'CSQ' does not exist in secondary vcf")
}
@Test def testMinMethodException = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:min")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:CSQ:min")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Type of field CSQ is not numeric")
}
@Test def testMaxMethodException = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:max")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:CSQ:max")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Type of field CSQ is not numeric")
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
index 5a12e9b579296b58a2764fdaa0b5b916717e384f..53aeddfaf1d6ba87f9e89ac29b31edff8fc5e01b 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
@@ -47,38 +47,44 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testGzOutputExplode(): Unit = {
- val tmpPath = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf.gz")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testVcfOutputExplode(): Unit = {
- val tmpPath = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testBcfOutputExplode(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".bcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testGzOutputStandard(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf.gz")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@Test def testVcfOutputStandard(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@Test def testBcfOutputStandard(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".bcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
index 685108d0cb7f31cebfcc4b998017ae0a4c91726f..3dfac894eeb591a84a31b3fd5bcfa88c34619192 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
@@ -28,7 +28,11 @@ trait Rscript extends Configurable {
} else {
val rScript: File = dir match {
case Some(dir) => new File(dir, script.getName)
- case _ => File.createTempFile(script.getName, ".R")
+ case _ => {
+ val file = File.createTempFile(script.getName, ".R")
+ file.deleteOnExit()
+ file
+ }
}
if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
diff --git a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index ad8ff00ee2e8a09026168efbf99f5926b4583c50..6bac74cdf9f3bf6148a78b05271593242d9b2d07 100644
--- a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -228,6 +228,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
object ConfigUtilsTest {
def writeTemp(text: String, extension: String): File = {
val file = File.createTempFile("TestConfigUtils.", extension)
+ file.deleteOnExit()
val w = new PrintWriter(file)
w.write(text)
w.close()
diff --git a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
index b748006c2800d5e86aad9e5f918a3d4bf5894c2c..0490b28db7dbf199a9b01c1b48c6783f11720f7d 100644
--- a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
@@ -39,6 +39,7 @@ class BedRecordListTest extends TestNGSuite with Matchers {
records.header shouldBe Nil
val tempFile = File.createTempFile("region", ".bed")
+ tempFile.deleteOnExit()
records.writeToFile(tempFile)
BedRecordList.fromFile(tempFile) shouldBe records
tempFile.delete()
@@ -50,6 +51,7 @@ class BedRecordListTest extends TestNGSuite with Matchers {
records.header shouldBe BedRecordListTest.ucscHeader.split("\n").toList
val tempFile = File.createTempFile("region", ".bed")
+ tempFile.deleteOnExit()
records.writeToFile(tempFile)
BedRecordList.fromFile(tempFile) shouldBe records
tempFile.delete()
@@ -129,13 +131,6 @@ class BedRecordListTest extends TestNGSuite with Matchers {
list.scatter(100).allRecords.size shouldBe 15
list.scatter(100).length shouldBe 1500
}
-
- @AfterClass
- def end: Unit = {
- BedRecordListTest.bedFile.delete()
- BedRecordListTest.corruptBedFile.delete()
- BedRecordListTest.bedFileUcscHeader.delete()
- }
}
object BedRecordListTest {
@@ -149,6 +144,9 @@ object BedRecordListTest {
|chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399 0,3601""".stripMargin
val bedFile = File.createTempFile("regions", ".bed")
+ bedFile.deleteOnExit()
val corruptBedFile = File.createTempFile("regions", ".bed")
+ corruptBedFile.deleteOnExit()
val bedFileUcscHeader = File.createTempFile("regions", ".bed")
+ bedFileUcscHeader.deleteOnExit()
}
\ No newline at end of file
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 195718d5de9f0b708c2bcbc64faaf927109c176f..f8b4dc6db0ff771d046ffe320a24a7c0d294b832 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -78,6 +78,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
if (config.contains("R1")) {
mapping.input_R1 = config("R1")
if (config.contains("R2")) mapping.input_R2 = config("R2")
+
+ inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
+ mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
+
mapping.init()
mapping.biopetScript()
addAll(mapping.functions)
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index c361908fa1110ef7133639e91912acab5cce0da9..407b6fb415a4dbce63a80228241b7a81df29cf36 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -97,6 +97,12 @@ class CarpTest extends TestNGSuite with Matchers {
object CarpTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
@@ -127,8 +133,8 @@ object CarpTest {
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "1_1_R1.fq",
- "R2" -> "1_1_R2.fq"
+ "R1" -> inputTouch("1_1_R1.fq"),
+ "R2" -> inputTouch("1_1_R2.fq")
)
)
)))
@@ -136,8 +142,8 @@ object CarpTest {
val sample2 = Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "2_1_R1.fq",
- "R2" -> "2_1_R2.fq"
+ "R1" -> inputTouch("2_1_R1.fq"),
+ "R2" -> inputTouch("2_1_R2.fq")
)
)
)))
@@ -145,12 +151,12 @@ object CarpTest {
val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "3_1_R1.fq",
- "R2" -> "3_1_R2.fq"
+ "R1" -> inputTouch("3_1_R1.fq"),
+ "R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> "3_2_R1.fq",
- "R2" -> "3_2_R2.fq"
+ "R1" -> inputTouch("3_2_R1.fq"),
+ "R2" -> inputTouch("3_2_R2.fq")
)
)
)))
@@ -158,8 +164,8 @@ object CarpTest {
val threatment1 = Map(
"samples" -> Map("threatment" -> Map("control" -> "control1", "libraries" -> Map(
"lib1" -> Map(
- "R1" -> "threatment_1_R1.fq",
- "R2" -> "threatment_1_R2.fq"
+ "R1" -> inputTouch("threatment_1_R1.fq"),
+ "R2" -> inputTouch("threatment_1_R2.fq")
)
)
)))
@@ -167,8 +173,8 @@ object CarpTest {
val control1 = Map(
"samples" -> Map("control1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "control_1_R1.fq",
- "R2" -> "control_1_R2.fq"
+ "R1" -> inputTouch("control_1_R1.fq"),
+ "R2" -> inputTouch("control_1_R2.fq")
)
)
)))
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 07c356b7a894d5797002751d264a4b24e3ba5e7e..7ae2730c2bd92c3c06e10ecb2452cc3d1e823933 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -85,6 +85,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
paired = input_R2.isDefined
+ inputFiles :+= new InputFile(input_R1)
+ input_R2.foreach(inputFiles :+= new InputFile(_))
+
if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
else R1_name = input_R1.getName
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 2cb3f0e7b36175d9bf7633d7d639e6b03612976f..7b6716024963be03f256eb31bfad2bf5bcdf769e 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -67,8 +67,8 @@ class FlexiprepTest extends TestNGSuite with Matchers {
), Map(FlexiprepTest.executables.toSeq: _*))
val flexiprep: Flexiprep = initPipeline(map)
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq" + (if (zipped) ".gz" else ""))
- if (paired) flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq" + (if (zipped) ".gz" else "")))
+ flexiprep.input_R1 = (if (zipped) FlexiprepTest.r1Zipped else FlexiprepTest.r1)
+ if (paired) flexiprep.input_R2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
flexiprep.sampleId = Some("1")
flexiprep.libId = Some("1")
flexiprep.script()
@@ -95,6 +95,16 @@ class FlexiprepTest extends TestNGSuite with Matchers {
object FlexiprepTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+
+ val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+ Files.touch(r1)
+ val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+ Files.touch(r2)
+ val r1Zipped = new File(outputDir, "input" + File.separator + "R1.fq.gz")
+ Files.touch(r1Zipped)
+ val r2Zipped = new File(outputDir, "input" + File.separator + "R2.fq.gz")
+ Files.touch(r2Zipped)
val executables = Map(
"seqstat" -> Map("exe" -> "test"),
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index c500757088d3c313190cb4a9b0eca65bfc48f9a4..d033594c6e42663427108baf12038b7eed6fb3f6 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -844,6 +844,8 @@ class Gentrap(val root: Configurable) extends QScript
def addJobs(): Unit = {
// create per-library alignment file
addAll(mappingJob.functions)
+ // Input file checking
+ inputFiles :::= mappingJob.inputFiles
// add bigwig track
addAll(bam2wigModule.functions)
qscript.addSummaryQScript(mappingJob)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index 1ce8465cae9c75dbcbed9c85374074202ff9b393..8871f481f3075d7eef52784583ccb5aadaa5b715 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
@@ -28,16 +28,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */
// FIXME: generalize piping instead of building something by hand like this!
// Better to do everything quick and dirty here rather than something half-implemented with the objects
-class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction { wrapper =>
+class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction with Reference { wrapper =>
override def configName = "customvarscan"
@Input(doc = "Input BAM file", required = true)
var input: File = null
- @Input(doc = "Reference FASTA file", required = true)
- var reference: File = config("reference")
-
@Output(doc = "Output VCF file", required = true)
var output: File = null
@@ -49,7 +46,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
this.input = List(wrapper.input)
override def configName = wrapper.configName
disableBaq = true
- reference = config("reference")
depth = Option(1000000)
outputMappingQuality = true
}
@@ -92,7 +88,9 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
}
override def beforeGraph(): Unit = {
+ super.beforeGraph()
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
+ deps :+= referenceFasta()
}
def cmdLine: String = {
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 140db66fd62dd850365b27137cc3df0891bd38a7..2b2ddaf259e8fa5ad382ef1aca1337826ecf0ad8 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -43,8 +43,8 @@ class GentrapTest extends TestNGSuite with Matchers {
/** Convenience method for making library config */
private def makeLibConfig(idx: Int, paired: Boolean = true) = {
- val files = Map("R1" -> "test_R1.fq")
- if (paired) (s"lib_$idx", files ++ Map("R2" -> "test_R2.fq"))
+ val files = Map("R1" -> GentrapTest.inputTouch("test_R1.fq"))
+ if (paired) (s"lib_$idx", files ++ Map("R2" -> GentrapTest.inputTouch("test_R2.fq")))
else (s"lib_$idx", files)
}
@@ -179,6 +179,12 @@ class GentrapTest extends TestNGSuite with Matchers {
object GentrapTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 9d508b12ce727acb0bdfdf52fc485b8e353e5dae..3c886ee3a7c04544953e02a29d960a9436559bcb 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -137,6 +137,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require(sampleId.isDefined, "Missing sample ID on mapping module")
require(libId.isDefined, "Missing library ID on mapping module")
+ inputFiles :+= new InputFile(input_R1)
+ input_R2.foreach(inputFiles :+= new InputFile(_))
+
paired = input_R2.isDefined
if (readgroupId == null) readgroupId = sampleId.get + "-" + libId.get
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 849bffcb6998f31e8d527af465de68775b6e11a4..3c28181101a75eafa1518e441fb457a5ae197099 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -79,11 +79,11 @@ class MappingTest extends TestNGSuite with Matchers {
val mapping: Mapping = initPipeline(map)
if (zipped) {
- mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq.gz")
- if (paired) mapping.input_R2 = Some(new File(mapping.outputDir, "bla_R2.fq.gz"))
+ mapping.input_R1 = MappingTest.r1Zipped
+ if (paired) mapping.input_R2 = Some(MappingTest.r2Zipped)
} else {
- mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq")
- if (paired) mapping.input_R2 = Some(new File(mapping.outputDir, "bla_R2.fq"))
+ mapping.input_R1 = MappingTest.r1
+ if (paired) mapping.input_R2 = Some(MappingTest.r2)
}
mapping.sampleId = Some("1")
mapping.libId = Some("1")
@@ -131,6 +131,16 @@ class MappingTest extends TestNGSuite with Matchers {
object MappingTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+
+ val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+ Files.touch(r1)
+ val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+ Files.touch(r2)
+ val r1Zipped = new File(outputDir, "input" + File.separator + "R1.fq.gz")
+ Files.touch(r1Zipped)
+ val r2Zipped = new File(outputDir, "input" + File.separator + "R2.fq.gz")
+ Files.touch(r2Zipped)
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
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 4aaee19c295de32dbc306a94cf6fecf63d1ba754..2ee8c3b1930aff553234f6f3860d7c13e0818783 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
@@ -88,6 +88,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.sampleId = Some(sampleId)
protected def addJobs(): Unit = {
+ inputFiles :+= new InputFile(inputFastq, config("R1_md5"))
+
flexiprep.outputDir = new File(libDir, "flexiprep/")
flexiprep.input_R1 = inputFastq
flexiprep.init()
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 3f65bf2a20864e2017f512981daa0d37aca52772..dafb2e1ccc5a72807aa37cc6858711afbfe78c23 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
@@ -136,51 +136,56 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
case (true, _) => mapping.foreach(mapping => {
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
+ inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
+ mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
})
- case (false, true) => config("bam_to_fastq", default = false).asBoolean match {
- case true =>
- val samToFastq = SamToFastq(qscript, config("bam"),
- new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
- new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
- samToFastq.isIntermediate = true
- qscript.add(samToFastq)
- mapping.foreach(mapping => {
- mapping.input_R1 = samToFastq.fastqR1
- mapping.input_R2 = Some(samToFastq.fastqR2)
- })
- case false =>
- val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
- val readGroups = inputSam.getFileHeader.getReadGroups
-
- val readGroupOke = readGroups.forall(readGroup => {
- if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
- if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
- readGroup.getSample == sampleId && readGroup.getLibrary == libId
- })
- inputSam.close()
-
- if (!readGroupOke) {
- if (config("correct_readgroups", default = false).asBoolean) {
- logger.info("Correcting readgroups, file:" + config("bam"))
- val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
- aorrg.RGID = sampleId + "-" + libId
- aorrg.RGLB = libId
- aorrg.RGSM = sampleId
- aorrg.isIntermediate = true
- qscript.add(aorrg)
- } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
- "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
- } else {
- val oldBamFile: File = config("bam")
- val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
- val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
- val baiLn = Ln(qscript, oldIndex, newIndex)
- add(baiLn)
-
- val bamLn = Ln(qscript, oldBamFile, bamFile.get)
- bamLn.deps :+= baiLn.output
- add(bamLn)
- }
+ case (false, true) => {
+ inputFiles :+= new InputFile(config("bam"), config("bam_md5"))
+ config("bam_to_fastq", default = false).asBoolean match {
+ case true =>
+ val samToFastq = SamToFastq(qscript, config("bam"),
+ new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
+ new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
+ samToFastq.isIntermediate = true
+ qscript.add(samToFastq)
+ mapping.foreach(mapping => {
+ mapping.input_R1 = samToFastq.fastqR1
+ mapping.input_R2 = Some(samToFastq.fastqR2)
+ })
+ case false =>
+ val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
+ val readGroups = inputSam.getFileHeader.getReadGroups
+
+ val readGroupOke = readGroups.forall(readGroup => {
+ if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
+ if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
+ readGroup.getSample == sampleId && readGroup.getLibrary == libId
+ })
+ inputSam.close()
+
+ if (!readGroupOke) {
+ if (config("correct_readgroups", default = false).asBoolean) {
+ logger.info("Correcting readgroups, file:" + config("bam"))
+ val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
+ aorrg.RGID = sampleId + "-" + libId
+ aorrg.RGLB = libId
+ aorrg.RGSM = sampleId
+ aorrg.isIntermediate = true
+ qscript.add(aorrg)
+ } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
+ "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
+ } else {
+ val oldBamFile: File = config("bam")
+ val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
+ val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
+ val baiLn = Ln(qscript, oldIndex, newIndex)
+ add(baiLn)
+
+ val bamLn = Ln(qscript, oldBamFile, bamFile.get)
+ bamLn.deps :+= baiLn.output
+ add(bamLn)
+ }
+ }
}
case _ => logger.warn("Sample: " + sampleId + " Library: " + libId + ", no reads found")
}
@@ -294,7 +299,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
addAll(vc.functions)
addSummaryQScript(vc)
- if (config("annotation", default = true).asBoolean) {
+ if (config("annotation", default = false).asBoolean) {
val toucan = new Toucan(this)
toucan.outputDir = new File(outputDir, "annotation")
toucan.inputVCF = vc.finalFile
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index 56b6bf172b2d122b2ccd70818d3f9f92161e270d..cff186c29e8776f4457ceb6787ea75efc61a8885 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -88,6 +88,12 @@ class ShivaTest extends TestNGSuite with Matchers {
object ShivaTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
@@ -131,8 +137,8 @@ object ShivaTest {
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "1_1_R1.fq",
- "R2" -> "1_1_R2.fq"
+ "R1" -> inputTouch("1_1_R1.fq"),
+ "R2" -> inputTouch("1_1_R2.fq")
)
)
)))
@@ -140,8 +146,8 @@ object ShivaTest {
val sample2 = Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "2_1_R1.fq",
- "R2" -> "2_1_R2.fq"
+ "R1" -> inputTouch("2_1_R1.fq"),
+ "R2" -> inputTouch("2_1_R2.fq")
)
)
)))
@@ -149,12 +155,12 @@ object ShivaTest {
val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "3_1_R1.fq",
- "R2" -> "3_1_R2.fq"
+ "R1" -> inputTouch("3_1_R1.fq"),
+ "R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> "3_2_R1.fq",
- "R2" -> "3_2_R2.fq"
+ "R1" -> inputTouch("3_2_R1.fq"),
+ "R2" -> inputTouch("3_2_R2.fq")
)
)
)))
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 0281d33f678804d7edd1620d204a0830d4f3201f..caeea0326d46e4b7673dae4a3d07f27c3cbd5f4e 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -61,7 +61,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
- pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+ pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !freebayes)
@@ -88,6 +88,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): File = {
+ val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+ Files.touch(file)
+ file
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 606853f933f6cd1263a0f44193e5ae0e615812df..7c3cc327858be60bb3d299e550c0f4244b656560 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -35,6 +35,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var inputVCF: File = _
def init(): Unit = {
+ inputFiles :+= new InputFile(inputVCF)
}
override def defaults = ConfigUtils.mergeMaps(Map(