fix non-required arguments for manwe

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala

@@ -19,7 +19,7 @@ class ManweAnnotateBed(val root: Configurable) extends Manwe {
   @Argument(doc = "Flag whether to wait for annotation to complete on the server")
   var waitToComplete: Boolean = false
 
-  @Argument(doc = "annotation queries")
+  @Argument(doc = "annotation queries", required = false)
   var queries: List[String] = Nil
 
   def subCommand = {

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala

@@ -19,7 +19,7 @@ class ManweAnnotateVcf(val root: Configurable) extends Manwe {
   @Argument(doc = "flag whether to wait for annotation to complete")
   var waitToComplete: Boolean = false
 
-  @Argument(doc = "annotation queries")
+  @Argument(doc = "annotation queries", required = false)
   var queries: List[String] = Nil
 
   def subCommand = {

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala

@@ -11,7 +11,7 @@ class ManweDataSourcesAnnotate(val root: Configurable) extends Manwe {
   @Argument(doc = "uri to data source to annotate")
   var uri: Option[String] = _
 
-  @Argument(doc = "list of queries")
+  @Argument(doc = "list of queries", required = false)
   var queries: List[String] = Nil
 
   @Argument(doc = "Flag whether to wait for annotation to complete on server")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala

@@ -13,7 +13,7 @@ class ManweSamplesAdd(val root: Configurable) extends Manwe {
   @Argument(doc = "the sample name")
   var name: Option[String] = _
 
-  @Argument(doc = "the sample groups [uris]")
+  @Argument(doc = "the sample groups [uris]", required = false)
   var group: List[String] = Nil
 
   @Argument(doc = "pool size")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala

@@ -13,7 +13,7 @@ class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
   @Argument(doc = "uri to sample to annotate")
   var uri: Option[String] = _
 
-  @Argument(doc = "Annotation queries")
+  @Argument(doc = "Annotation queries", required = false)
   var queries: List[String] = Nil
 
   def subCommand = {

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala

@@ -10,10 +10,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
  */
 class ManweSamplesList(val root: Configurable) extends Manwe {
 
-  @Argument(doc = "filter by user URI")
+  @Argument(doc = "filter by user URI", required = false)
   var user: Option[String] = None
 
-  @Argument(doc = "filter by group URI")
+  @Argument(doc = "filter by group URI", required = false)
   var group: List[String] = Nil
 
   var onlyPublic: Boolean = false

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala

@@ -30,6 +30,8 @@ class ManweTest extends TestNGSuite with Matchers {
     manwe.output = out
     manwe.bed = bed
     manwe.alreadyUploaded = false
+    manwe.cmd should equal(s"manwe annotate-bed ${bed.getAbsolutePath} -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
+
     manwe.queries = List("/uri/1&&/uri/2")
     manwe.cmd should equal(s"manwe annotate-bed ${bed.getAbsolutePath} -q /uri/1&&/uri/2 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
 
@@ -55,6 +57,8 @@ class ManweTest extends TestNGSuite with Matchers {
     manwe.output = out
     manwe.vcf = vcf
     manwe.alreadyUploaded = false
+    manwe.cmd should equal(s"manwe annotate-vcf ${vcf.getAbsolutePath} -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
+
     manwe.queries = List("/uri/1&&/uri/2")
     manwe.cmd should equal(s"manwe annotate-vcf ${vcf.getAbsolutePath} -q /uri/1&&/uri/2 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
 
@@ -77,6 +81,8 @@ class ManweTest extends TestNGSuite with Matchers {
     manwe.manweConfig = new File("/usr/local/nonexistent.conf")
     manwe.output = out
     manwe.uri = Some("/uri/1")
+    manwe.cmd should equal(s"manwe data-sources annotate /uri/1 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
+
     manwe.queries = List("/uri/1&&/uri/2")
     manwe.cmd should equal(s"manwe data-sources annotate /uri/1 -q /uri/1&&/uri/2 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
 

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -109,7 +109,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     val splits = sampleIds.map(x => {
       val view = new BcftoolsView(this)
       view.input = vcf
-      view.output = swapExt(vcf, ".vcf.gz", s"$x.vcf.gz")
+      view.output = swapExt(outputDir, vcf, ".vcf.gz", s"$x.vcf.gz")
       view.samples = List(x)
       view.minAC = Some(1)
       add(view)
@@ -147,7 +147,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
 
     val annotate = new ManweAnnotateVcf(this)
     annotate.vcf = vcf
-    annotate.queries = annotationQueries
+    if (annotationQueries.nonEmpty) {
+      annotate.queries = annotationQueries
+    }
     annotate.waitToComplete = true
     annotate.output = swapExt(outputDir, vcf, ".vcf.gz", ".tmp.annot")
     add(annotate)