addressed review comments

biopet/biopet.wdl

@@ -452,7 +452,45 @@ task VcfStats {
             "/sample_compare/genotype.non_ref.abs.tsv"
         File? sampleCompareGenotypeRefAbs = outputDir + "/sample_compare/genotype.ref.abs.tsv"
         File? sampleCompareGenotypeRel = outputDir + "/sample_compare/genotype.rel.tsv"
-        Array[File] allStats = glob(outputDir + "/*")
+        # A glob is easier, but duplicates all the outputs
+        Array[File] allStats = select_all([
+            general,
+            genotype,
+            sampleDistributionAvailableAggregate,
+            sampleDistributionAvailable,
+            sampleDistributionCalledAggregate,
+            sampleDistributionCalled,
+            sampleDistributionFilteredAggregate,
+            sampleDistributionFiltered,
+            sampleDistributionHetAggregate,
+            sampleDistributionHetNoNRefAggregate,
+            sampleDistributionHetNonRef,
+            sampleDistributionHet,
+            sampleDistributionHomAggregate,
+            sampleDistributionHomRefAggregate,
+            sampleDistributionHomRef,
+            sampleDistributionHom,
+            sampleDistributionHomVarAggregate,
+            sampleDistributionHomVar,
+            sampleDistributionMixedAggregate,
+            sampleDistributionMixed,
+            sampleDistributionNoCallAggregate,
+            sampleDistributionNoCall,
+            sampleDistributionNonInformativeAggregate,
+            sampleDistributionNonInformative,
+            sampleDistributionToalAggregate,
+            sampleDistributionTotal,
+            sampleDistributionVariantAggregate,
+            sampleDistributionVariant,
+            sampleCompareAlleleAbs,
+            sampleCompareAlleleNonRefAbs,
+            sampleCompareAlleleRefAbs,
+            sampleCompareAlleleRel,
+            sampleCompareGenotypeAbs,
+            sampleCompareGenotypeNonRefAbs,
+            sampleCompareGenotypeRefAbs,
+            sampleCompareGenotypeRel
+        ])
     }
 
     runtime {

bwa.wdl

@@ -34,7 +34,7 @@ task Mem {
 
     output {
         File outputBam = outputPath
-        File outputBamIndex = sub(outputPath, ".bam$", ".bai")
+        File outputBamIndex = sub(outputPath, "\.bam$", ".bai")
     }
 
     runtime{

picard.wdl

@@ -230,7 +230,7 @@ task GatherBamFiles {
 
     output {
         File outputBam = outputBamPath
-        File outputBamIndex = sub(outputBamPath, ".bam$", ".bai")
+        File outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
         File outputBamMd5 = outputBamPath + ".md5"
     }
 
@@ -313,7 +313,7 @@ task MarkDuplicates {
 
     output {
         File outputBam = outputBamPath
-        File outputBamIndex = sub(outputBamPath, ".bam$", ".bai")
+        File outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
         File outputBamMd5 = outputBamPath + ".md5"
         File metricsFile = metricsPath
     }