Fixinf nullpointers on unit tests

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -114,6 +114,7 @@ object BamMetricsTest {
   copyFile("ref.fa.fai")
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "refFlat" -> "bla.refFlat",
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "samtools" -> Map("exe" -> "test"),

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -144,6 +144,7 @@ object BastyTest {
   copyFile("ref.fa.fai")
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "cache" -> true,
     "dir" -> "test",

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -63,6 +63,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
   /** Returns the extension to make the report */
   def reportClass: Option[ReportBuilderExtension] = None
 
+  val skipWriteDependencies: Boolean = config("skip_write_dependencies", default = false)
+
   /** Script from queue itself, final to force some checks for each pipeline and write report */
   final def script() {
     outputDir = config("output_dir")
@@ -122,7 +124,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       }
     })
 
-    WriteDependencies.writeDependencies(functions, new File(outputDir, ".log"), qSettings.runName)
+    if (!skipWriteDependencies) WriteDependencies.writeDependencies(functions, new File(outputDir, ".log"), qSettings.runName)
 
     Logging.checkErrors()
     logger.info("Script complete without errors")

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -57,7 +57,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     for (q <- qscript.summaryQScripts)
       deps :+= q.summaryFile
     for ((_, l) <- qscript.summarizables; s <- l) s match {
-      case f: QFunction => deps :+= f.firstOutput
+      case f: QFunction => try {
+        deps :+= f.firstOutput
+      }  catch {
+        case e: NullPointerException => logger.warn("Queue values are not init")
+      }
       case _            =>
     }
 

carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -117,6 +117,7 @@ object CarpTest {
   copyFile("ref.fa.fai")
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -115,6 +115,7 @@ object FlexiprepTest {
   Files.touch(r2Zipped)
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "seqstat" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -234,6 +234,7 @@ object TestGearsSingle {
   bam.deleteOnExit()
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "centrifuge" -> Map("exe" -> "test", "centrifuge_index" -> "test"),
     "centrifugekreport" -> Map("exe" -> "test"),

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala

@@ -113,6 +113,7 @@ object GearsTest {
   Files.touch(bam)
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "output_dir" -> outputDir,
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala

@@ -141,7 +141,9 @@ object DownloadGenomesTest {
   val outputDir = Files.createTempDir()
   outputDir.deleteOnExit()
 
-  val config = Map("output_dir" -> outputDir,
+  val config = Map(
+    "skip_write_dependencies" -> true,
+    "output_dir" -> outputDir,
     "bwa" -> Map("exe" -> "test"),
     "star" -> Map("exe" -> "test"),
     "hisat2build" -> Map("exe" -> "test"),

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -186,6 +186,7 @@ object GentrapTest {
   copyFile("ref.fa.fai")
 
   val executables: Map[String, Any] = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "refFlat" -> (outputDir + File.separator + "ref.fa"),
     "annotation_gtf" -> (outputDir + File.separator + "ref.fa"),

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -75,6 +75,7 @@ object GwasTestTest {
   }
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> reference.toString,
     "phenotype_file" -> phenotypeFile.toString,
     "output_dir" -> outputDir,

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

@@ -93,6 +93,7 @@ object Impute2VcfTest {
   }
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> reference.toString,
     "phenotype_file" -> phenotypeFile.toString,
     "output_dir" -> outputDir,

kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala

@@ -112,6 +112,7 @@ object KopisuTest {
   Files.touch(new File(controlDir, "test.txt"))
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "output_dir" -> outputDir,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -128,6 +128,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
   }
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "db" -> "test",
     "bowtie_index" -> (outputDir + File.separator + "ref"),

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -184,6 +184,7 @@ object MultisampleMappingTestTrait {
   copyFile("empty.sam")
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "cache" -> true,
     "dir" -> "test",

sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala

@@ -131,6 +131,7 @@ object SageTest {
   copyFile("ref.fa.fai")
 
   val config: Map[String, Any] = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "output_dir" -> outputDir.getAbsolutePath,
     "fastqc" -> Map("exe" -> "test"),

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala

@@ -198,6 +198,7 @@ object ShivaSvCallingTest {
   copyFile("ref.fa.fai")
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "output_dir" -> outputDir,
     "cache" -> true,

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -191,6 +191,7 @@ object ShivaTest {
   copyFile("ref.fa.fai")
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "cache" -> true,
     "dir" -> "test",

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -230,6 +230,7 @@ object ShivaVariantcallingTest {
   copyFile("ref.fa.fai")
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "output_dir" -> outputDir,
     "cache" -> true,

tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala

@@ -119,6 +119,7 @@ object TinyCapTest {
   Files.touch(annotationRefflat)
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "output_dir" -> outputDir,
     "reference_fasta" -> (referenceFasta.getAbsolutePath),
     "bowtie_index" -> (bowtieIndex.getAbsolutePath),

toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala

@@ -107,6 +107,7 @@ object ToucanTest {
   exacVcfFile.deleteOnExit()
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> resourcePath("/fake_chrQ.fa"),
     "output_dir" -> outputDir,
     "gatk_jar" -> "test",