fix variable typo

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

@@ -149,7 +149,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   private[core] var _inputAsStdin = false
   def inputAsStdin = _inputAsStdin
   private[core] var _outputAsStdout = false
-  def outputAsStsout = _outputAsStdout
+  def outputAsStdout = _outputAsStdout
 
   /**
     * This operator sends stdout to `that` and combine this into 1 command line function

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala

@@ -27,7 +27,7 @@ class BiopetPipeTest extends TestNGSuite with Matchers {
     def cmdLine =
       "pipe1" +
         (if (!inputAsStdin) " input1 " else "") +
-        (if (!outputAsStsout) " output1 " + "")
+        (if (!outputAsStdout) " output1 " + "")
   }
 
   class Pipe2 extends BiopetCommandLineFunction {
@@ -35,7 +35,7 @@ class BiopetPipeTest extends TestNGSuite with Matchers {
     def cmdLine =
       "pipe2" +
         (if (!inputAsStdin) " input2 " else "") +
-        (if (!outputAsStsout) " output2 " + "")
+        (if (!outputAsStdout) " output2 " + "")
   }
 
   @Test def testPipeCommands: Unit = {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala

@@ -44,7 +44,7 @@ class Awk(val parent: Configurable) extends BiopetCommandLineFunction with Versi
     executable +
       required(command) +
       (if (inputAsStdin) "" else required(input)) +
-      (if (outputAsStsout) "" else " > " + required(output))
+      (if (outputAsStdout) "" else " > " + required(output))
 }
 
 object Awk {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala

@@ -36,12 +36,12 @@ class Bgzip(val parent: Configurable) extends BiopetCommandLineFunction {
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     if (input.isEmpty && !inputAsStdin) Logging.addError("Input is missing for Bgzip")
-    if (output == null && !outputAsStsout) Logging.addError("Output is missing for Bgzip")
+    if (output == null && !outputAsStdout) Logging.addError("Output is missing for Bgzip")
   }
 
   def cmdLine =
     required(executable) +
       conditional(f, "-f") +
       " -c " + repeat(input) +
-      (if (outputAsStsout) "" else " > " + required(output))
+      (if (outputAsStdout) "" else " > " + required(output))
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

@@ -38,7 +38,7 @@ class Cat(val parent: Configurable) extends BiopetCommandLineFunction {
   def cmdLine =
     required(executable) +
       (if (inputAsStdin) "" else repeat(input)) +
-      (if (outputAsStsout) "" else (if (appending) " >> " else " > ") + required(output))
+      (if (outputAsStdout) "" else (if (appending) " >> " else " > ") + required(output))
 }
 
 /**

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala

@@ -34,5 +34,5 @@ class Curl(val parent: Configurable) extends BiopetCommandLineFunction with Vers
   def versionRegex = """curl (\w+\.\w+\.\w+) .*""".r
 
   def cmdLine: String =
-    required(executable) + required(url) + (if (outputAsStsout) "" else " > " + required(output))
+    required(executable) + required(url) + (if (outputAsStdout) "" else " > " + required(output))
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -165,7 +165,7 @@ class Cutadapt(val parent: Configurable)
       optional("--untrimmed-paired-output", untrimmedPairedOutput) +
       // input / output
       required(fastqInput) +
-      (if (outputAsStsout) ""
+      (if (outputAsStdout) ""
        else
          required("--output", fastqOutput) +
            " > " + required(statsOutput))

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

@@ -206,5 +206,5 @@ class Freebayes(val parent: Configurable)
       conditional(debug, "--debug") +
       optional("--haplotype-length", haplotypeLength) +
       (if (inputAsStdin) required("--stdin") else "") +
-      (if (outputAsStsout) "" else optional("--vcf", outputVcf))
+      (if (outputAsStdout) "" else optional("--vcf", outputVcf))
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala

@@ -38,6 +38,6 @@ class GffRead(val parent: Configurable) extends BiopetCommandLineFunction {
   def cmdLine =
     executable +
       (if (inputAsStdin) "" else required(input)) +
-      (if (outputAsStsout) "" else required("-o", output)) +
+      (if (outputAsStdout) "" else required("-o", output)) +
       conditional(T, "-T")
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala

@@ -46,7 +46,7 @@ class Grep(val parent: Configurable) extends BiopetCommandLineFunction {
       conditional(perlRegexp, "-P") +
       required(grepFor) +
       (if (inputAsStdin) "" else required(input)) +
-      (if (outputAsStsout) "" else " > " + required(output))
+      (if (outputAsStdout) "" else " > " + required(output))
 }
 
 object Grep {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala

@@ -51,5 +51,5 @@ class GtfToGenePred(val parent: Configurable) extends BiopetCommandLineFunction
       conditional(simple, "-simple") +
       conditional(geneNameAsName2, "-geneNameAsName2") +
       repeat(inputGtfs) +
-      (if (outputAsStsout) required("/dev/stdout") else required(outputGenePred))
+      (if (outputAsStdout) required("/dev/stdout") else required(outputGenePred))
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -35,7 +35,7 @@ class Gzip(val parent: Configurable) extends BiopetCommandLineFunction with Vers
   def cmdLine =
     required(executable) + " -c " +
       (if (inputAsStdin) "" else repeat(input)) +
-      (if (outputAsStsout) "" else " > " + required(output))
+      (if (outputAsStdout) "" else " > " + required(output))
 }
 
 object Gzip {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala

@@ -46,6 +46,6 @@ class Sed(val parent: Configurable) extends BiopetCommandLineFunction with Versi
     executable +
       repeat("-e", expressions) +
       (if (inputAsStdin) "" else required(inputFile)) +
-      (if (outputAsStsout) "" else " > " + required(outputFile))
+      (if (outputAsStdout) "" else " > " + required(outputFile))
 
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -78,13 +78,13 @@ class Sickle(val parent: Configurable)
     cmd +
       (if (inputAsStdin) required("-f", new File("/dev/stdin")) else required("-f", inputR1)) +
       required("-t", qualityType) +
-      (if (outputAsStsout) required("-o", new File("/dev/stdout")) else required("-o", outputR1)) +
+      (if (outputAsStdout) required("-o", new File("/dev/stdout")) else required("-o", outputR1)) +
       optional("-q", qualityThreshold) +
       optional("-l", lengthThreshold) +
       conditional(noFiveprime, "-x") +
       conditional(discardN, "-n") +
-      conditional(quiet || outputAsStsout, "--quiet") +
-      (if (outputAsStsout) "" else " > " + required(outputStats))
+      conditional(quiet || outputAsStdout, "--quiet") +
+      (if (outputAsStdout) "" else " > " + required(outputStats))
   }
 
   override def summaryDeps = outputStats :: super.summaryDeps

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

@@ -39,7 +39,7 @@ class Zcat(val parent: Configurable) extends BiopetCommandLineFunction with Vers
   def cmdLine =
     required(executable) +
       (if (inputAsStdin) "" else repeat(input)) +
-      (if (outputAsStsout) "" else (if (appending) " >> " else " > ") + required(output))
+      (if (outputAsStdout) "" else (if (appending) " >> " else " > ") + required(output))
 }
 
 object Zcat {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

@@ -82,6 +82,6 @@ class BcftoolsCall(val parent: Configurable) extends Bcftools {
       optional("-P", P) +
       conditional(X, "-X") +
       conditional(Y, "-Y") +
-      (if (outputAsStsout) "" else required("-o", output)) +
+      (if (outputAsStdout) "" else required("-o", output)) +
       (if (inputAsStdin) "-" else required(input))
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala

@@ -49,7 +49,7 @@ class BcftoolsMerge(val parent: Configurable) extends Bcftools {
   def cmdLine =
     required(executable) +
       required("merge") +
-      (if (outputAsStsout) "" else required("-o", output)) +
+      (if (outputAsStdout) "" else required("-o", output)) +
       conditional(forcesamples, "--force-samples") +
       conditional(printheader, "--print-header") +
       optional("--use-header", useheader) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -59,7 +59,7 @@ class BedtoolsCoverage(val parent: Configurable) extends Bedtools with Reference
       conditional(sorted, "-sorted") +
       (if (sorted) required("-g", BedtoolsCoverage.getGenomeFile(referenceFai, jobTempDir))
        else "") +
-      (if (outputAsStsout) "" else " > " + required(output))
+      (if (outputAsStdout) "" else " > " + required(output))
 
 }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala

@@ -37,6 +37,6 @@ class BedtoolsSort(val parent: Configurable) extends Bedtools with Reference {
   def cmdLine =
     required(executable) + required("sort") + required("-i", input) +
       optional("-faidx", faidx) +
-      (if (outputAsStsout) "" else " > " + required(output))
+      (if (outputAsStdout) "" else " > " + required(output))
 
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala

@@ -256,5 +256,5 @@ class Bowtie2(val parent: Configurable)
             optional("-2", r2)
         case _ => required("-U", R1)
       }) +
-      (if (outputAsStsout) "" else required("-S", output))
+      (if (outputAsStdout) "" else required("-S", output))
 }