Merge branch 'fix-tagged_files' into 'develop'

Fixed tagged files

Fixes #339 

See merge request !394

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala

@@ -69,7 +69,7 @@ class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterG
   override def cmdLine = super.cmdLine +
     repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-V", variant, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
     optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
     conditional(convertToBasePairResolution, "-bpResolution", escape = true, format = "%s") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala

@@ -129,7 +129,7 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
     optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
     conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala

@@ -419,7 +419,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
     optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
     optional("-likelihoodEngine", likelihoodCalculationEngine, spaceSeparated = true, escape = true, format = "%s") +
     optional("-hksr", heterogeneousKmerSizeResolution, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
     conditional(dontTrimActiveRegions, "-dontTrimActiveRegions", escape = true, format = "%s") +
     optional("-maxDiscARExtension", maxDiscARExtension, spaceSeparated = true, escape = true, format = "%s") +
     optional("-maxGGAARExtension", maxGGAARExtension, spaceSeparated = true, escape = true, format = "%s") +
@@ -444,7 +444,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
     repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
     optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
     optional("-gt_mode", genotyping_mode, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-alleles", alleles), alleles, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-alleles", alleles.getOrElse(null)), alleles, spaceSeparated = true, escape = true, format = "%s") +
     optional("-contamination", contamination_fraction_to_filter, spaceSeparated = true, escape = true, format = contamination_fraction_to_filterFormat) +
     optional("-contaminationFile", contamination_fraction_per_sample_file, spaceSeparated = true, escape = true, format = "%s") +
     optional("-pnrm", p_nonref_model, spaceSeparated = true, escape = true, format = "%s") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala

@@ -218,8 +218,8 @@ class SelectVariants(val root: Configurable) extends CommandLineGATK with Scatte
 
   override def cmdLine = super.cmdLine +
     required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-disc", discordance), discordance, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-conc", concordance), concordance, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-disc", discordance.getOrElse(null)), discordance, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-conc", concordance.getOrElse(null)), concordance, spaceSeparated = true, escape = true, format = "%s") +
     optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-sn", sample_name, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-se", sample_expressions, spaceSeparated = true, escape = true, format = "%s") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala

@@ -276,7 +276,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
     conditional(ignoreSNPAlleles, "-ignoreSNPAlleles", escape = true, format = "%s") +
     conditional(allReadsSP, "-dl", escape = true, format = "%s") +
     conditional(ignoreLaneInfo, "-ignoreLane", escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-referenceCalls", reference_sample_calls), reference_sample_calls, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-referenceCalls", reference_sample_calls.getOrElse(null)), reference_sample_calls, spaceSeparated = true, escape = true, format = "%s") +
     optional("-refsample", reference_sample_name, spaceSeparated = true, escape = true, format = "%s") +
     optional("-minqs", min_quality_score, spaceSeparated = true, escape = true, format = "%s") +
     optional("-maxqs", max_quality_score, spaceSeparated = true, escape = true, format = "%s") +
@@ -291,14 +291,14 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
     repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
     optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
     optional("-gt_mode", genotyping_mode, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-alleles", alleles), alleles, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-alleles", alleles.getOrElse(null)), alleles, spaceSeparated = true, escape = true, format = "%s") +
     optional("-contamination", contamination_fraction_to_filter, spaceSeparated = true, escape = true, format = contamination_fraction_to_filterFormat) +
     optional("-contaminationFile", contamination_fraction_per_sample_file, spaceSeparated = true, escape = true, format = "%s") +
     optional("-pnrm", p_nonref_model, spaceSeparated = true, escape = true, format = "%s") +
     optional("-logExactCalls", exactcallslog, spaceSeparated = true, escape = true, format = "%s") +
     optional("-out_mode", output_mode, spaceSeparated = true, escape = true, format = "%s") +
     conditional(allSitePLs, "-allSitePLs", escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
     optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-onlyEmitSamples", onlyEmitSamples, spaceSeparated = true, escape = true, format = "%s") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala

@@ -104,8 +104,8 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
 
   override def cmdLine = super.cmdLine +
     required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile.getOrElse()), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse()), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-resource", resource, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
     optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala

@@ -135,8 +135,8 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
     optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-eval", eval, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+    optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard.getOrElse(null)), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-select", select_exps, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-selectName", select_names, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-sn", sample, spaceSeparated = true, escape = true, format = "%s") +