update -M and -A flags to be inputs and attributes unnecessarily marked as optional

update changelog

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
 + Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
 + Cutadapt: Fix issues with read2output when using single-end reads.
 + Add feature type, idattr and additional attributes to htseq-count.

vardict.wdl

@@ -20,10 +20,12 @@ task VarDict {
         Int endColumn = 3
         Int geneColumn = 4
 
-        Float? mappingQuality = 20
-        Int? minimumTotalDepth = 8
-        Int? minimumVariantDepth = 4
-        Float? minimumAlleleFrequency = 0.02
+        Boolean outputCandidateSomaticOnly = true
+        Boolean outputAllVariantsAtSamePosition = true
+        Float mappingQuality = 20
+        Int minimumTotalDepth = 8
+        Int minimumVariantDepth = 4
+        Float minimumAlleleFrequency = 0.02
 
         Int threads = 1
         Int memory = 16
@@ -50,8 +52,8 @@ task VarDict {
         ~{true="var2vcf_paired.pl" false="var2vcf_valid.pl" defined(normalBam)} \
         -N "~{tumorSampleName}~{"|" + normalSampleName}" \
         ~{true="" false="-E" defined(normalBam)} \
-        -M \
-        -A \
+        ~{true="-M" false="" outputCandidateSomaticOnly} \
+        ~{true="-A" false="" outputAllVariantsAtSamePosition} \
         -Q ~{mappingQuality} \
         -d ~{minimumTotalDepth} \
         -v ~{minimumVariantDepth} \