Fixed unit tests

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -93,6 +93,12 @@ 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)
@@ -136,8 +142,8 @@ 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")
       )
     )
     )))
@@ -145,8 +151,8 @@ 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")
       )
     )
     )))
@@ -154,12 +160,12 @@ 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")
       )
     )
     )))

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)

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)

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

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")
       )
     )
     )))

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"),

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)

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)

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")
       )
     )
     )))

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)