Added piping to freebayes

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

@@ -149,7 +149,6 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
     optional("--contamination-estimates", contamination_estimates) +
     optional("--variant-input", variant_input) +
     optional("--haplotype-basis-alleles", haplotype_basis_alleles) +
-    optional("--vcf", outputVcf) +
     optional("--pvar", pvar) +
     optional("--theta", theta) +
     optional("--ploidy", ploidy) +
@@ -202,5 +201,7 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
     conditional(harmonic_indel_quality, "--harmonic-indel-quality") +
     conditional(genotype_qualities, "--genotype-qualities") +
     conditional(debug, "--debug") +
-    optional("--haplotype-length", haplotypeLength)
+    optional("--haplotype-length", haplotypeLength) +
+    (if (inputAsStdin) required("--stdin") else "") +
+    (if (outputAsStsout) "" else optional("--vcf", outputVcf))
 }

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala

@@ -14,15 +14,9 @@ class Freebayes(val root: Configurable) extends Variantcaller {
     val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(this)
     fb.bamfiles = inputBams.values.toList
     fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
-    fb.isIntermediate = true
-    add(fb)
+    //fb.isIntermediate = true
+    add(fb | new Bgzip(this) > outputFile)
 
-    //TODO: need piping for this, see also issue #114
-    val bz = new Bgzip(this)
-    bz.input = List(fb.outputVcf)
-    bz.output = outputFile
-    add(bz)
-
-    add(Tabix.apply(this, bz.output))
+    add(Tabix.apply(this, outputFile))
   }
 }