Merge branch 'develop' into optional-indexing

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 5.0.0-dev
 ---------------------------
++ survivor: replace integer boolean type to logical true or false value.
 + vt: Add option to ignore masked reference.
 + bcftools: add sorting and annotation
 + Bam2fastx: Input bam and index are now arrays.

survivor.wdl

@@ -27,9 +27,9 @@ task Merge {
         Array[File] filePaths
         Int breakpointDistance = 1000
         Int suppVecs = 2
-        Int svType = 1
-        Int strandType = 1
-        Int distanceBySvSize = 0
+        Boolean svType = true
+        Boolean strandType = true
+        Boolean distanceBySvSize = false
         Int minSize = 30
         String outputPath = "./survivor/merged.vcf"
         String memory = "24G"
@@ -45,9 +45,9 @@ task Merge {
         fileList \
         ~{breakpointDistance} \
         ~{suppVecs} \
-        ~{svType} \
-        ~{strandType} \
-        ~{distanceBySvSize} \
+        ~{true=1 false=0 svType} \
+        ~{true=1 false=0 strandType} \
+        ~{true=1 false=0 distanceBySvSize} \
         ~{minSize} \
         ~{outputPath}
     }