Merge branch 'fix-BIOPET-484' into 'develop'

Changes to the documentation for developers

BIOPET-484 Issue in JIRA

See merge request !488

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

@@ -141,7 +141,7 @@ object WriteDependencies extends Logging with Configurable {
 
     val jobsDeps = jobs.map(x => x._1 -> (x._2("depends_on_jobs") match {
       case l: List[_] => l.map(_.toString)
-      case _ => throw new IllegalStateException("Value 'depends_on_jobs' is not a list")
+      case _          => throw new IllegalStateException("Value 'depends_on_jobs' is not a list")
     }))
     val jobsWriter = new PrintWriter(new File(outputDir, s"$prefix.jobs.json"))
     jobsWriter.println(ConfigUtils.mapToJson(jobsDeps).spaces2)

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

@@ -59,10 +59,10 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     for ((_, l) <- qscript.summarizables; s <- l) s match {
       case f: QFunction => try {
         deps :+= f.firstOutput
-      }  catch {
+      } catch {
         case e: NullPointerException => logger.warn("Queue values are not init")
       }
-      case _            =>
+      case _ =>
     }
 
     jobOutputFile = new File(out.getParentFile, ".%s.%s.out".format(out.getName, analysisName))

docs/developer/getting-started.md

@@ -16,17 +16,17 @@ Make sure both tools are installed in your local maven repository. To do this on
 
 ```bash
 # Replace 'mvn' with the location of you maven executable or put it in your PATH with the export command.
-git clone https://github.com/broadgsa/gatk-protected
-cd gatk-protected
-git checkout 3.4
-# The GATK version is bound to a version of Biopet. Biopet 0.5.0 uses Gatk 3.4
+git clone https://github.com/broadgsa/gatk
+cd gatk
+git checkout 3.6
+# The GATK version is bound to a version of Biopet. Biopet 0.7.0 uses Gatk 3.6
 mvn clean install
 
 cd ..
 
 git clone https://github.com/biopet/biopet.git
 cd biopet
-git checkout 0.5.0
+git checkout 0.7.0
 mvn -DskipTests=true clean install
 ```
 

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -19,11 +19,11 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
-import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
+import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 }
+import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
+import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
 import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics