Convert more to biopet values

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -22,64 +22,54 @@ class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGat
   @Gather(classOf[BamGatherFunction])
   var out: File = _
 
-  /** Automatically generated index for out */
-  @Output(fullName = "outIndex", shortName = "", doc = "Automatically generated index for out", required = false, exclusiveOf = "", validation = "")
-  @Gather(enabled = false)
-  private var outIndex: File = _
-
-  /** Automatically generated md5 for out */
-  @Output(fullName = "outMD5", shortName = "", doc = "Automatically generated md5 for out", required = false, exclusiveOf = "", validation = "")
-  @Gather(enabled = false)
-  private var outMD5: File = _
-
   /** Exclude all reads with this read group from the output */
   @Argument(fullName = "readGroup", shortName = "readGroup", doc = "Exclude all reads with this read group from the output", required = false, exclusiveOf = "", validation = "")
-  var readGroup: String = _
+  var readGroup: Option[String] = config("readGroup", default = false)
 
   /** Exclude all reads with this platform from the output */
   @Argument(fullName = "platform", shortName = "platform", doc = "Exclude all reads with this platform from the output", required = false, exclusiveOf = "", validation = "")
-  var platform: String = _
+  var platform: Option[String] = config("platform")
 
   /** Print the first n reads from the file, discarding the rest */
   @Argument(fullName = "number", shortName = "n", doc = "Print the first n reads from the file, discarding the rest", required = false, exclusiveOf = "", validation = "")
-  var number: Option[Int] = None
+  var number: Option[Int] = config("number")
 
   /** File containing a list of samples (one per line). Can be specified multiple times */
   @Argument(fullName = "sample_file", shortName = "sf", doc = "File containing a list of samples (one per line). Can be specified multiple times", required = false, exclusiveOf = "", validation = "")
-  var sample_file: Seq[File] = Nil
+  var sample_file: List[File] = config("sample_file", default = Nil)
 
   /** Sample name to be included in the analysis. Can be specified multiple times. */
   @Argument(fullName = "sample_name", shortName = "sn", doc = "Sample name to be included in the analysis. Can be specified multiple times.", required = false, exclusiveOf = "", validation = "")
-  var sample_name: Seq[String] = Nil
+  var sample_name: List[String] = config("sample_name", default = Nil)
 
   /** Simplify all reads */
   @Argument(fullName = "simplify", shortName = "s", doc = "Simplify all reads", required = false, exclusiveOf = "", validation = "")
-  var simplify: Boolean = _
+  var simplify: Boolean = config("simplify", default = false)
 
   /** Don't output a program tag */
   @Argument(fullName = "no_pg_tag", shortName = "npt", doc = "Don't output a program tag", required = false, exclusiveOf = "", validation = "")
-  var no_pg_tag: Boolean = _
+  var no_pg_tag: Boolean = config("no_pg_tag", default = false)
 
   /** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
   @Argument(fullName = "filter_reads_with_N_cigar", shortName = "filterRNC", doc = "Filter out reads with CIGAR containing the N operator, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
-  var filter_reads_with_N_cigar: Boolean = _
+  var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
 
   /** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
   @Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
-  var filter_mismatching_base_and_quals: Boolean = _
+  var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
 
   /** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
-  var filter_bases_not_stored: Boolean = _
+  var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
   override def freezeFieldValues() {
     super.freezeFieldValues()
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
       if (!disable_bam_indexing)
-        outIndex = new File(out.getPath.stripSuffix(".bam") + ".bai")
+        outputFiles :+= new File(out.getPath.stripSuffix(".bam") + ".bai")
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
       if (generate_md5)
-        outMD5 = new File(out.getPath + ".md5")
+        outputFiles :+= new File(out.getPath + ".md5")
   }
 
   override def cmdLine = super.cmdLine +

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -116,14 +116,14 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
 
     if (config("use_analyze_covariates", default = false).asBoolean) {
       val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after"))
-      baseRecalibratorAfter.BQSR = baseRecalibrator.out
+      baseRecalibratorAfter.BQSR = Some(baseRecalibrator.out)
       add(baseRecalibratorAfter)
 
       add(AnalyzeCovariates(this, baseRecalibrator.out, baseRecalibratorAfter.out, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
     }
 
     val printReads = PrintReads(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
-    printReads.BQSR = baseRecalibrator.out
+    printReads.BQSR = Some(baseRecalibrator.out)
     printReads.isIntermediate = isIntermediate
     add(printReads)