diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d1805edaf96b3499803ba89d9e6a3846c5c31ed..121c876817134881b5ca408fc809cd90af236d80 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/survivor.wdl b/survivor.wdl index e5ac7b5bfb3bf8b2a9230f6c65f790287a4bafb8..b9583009538b76ebc77ec51f85ce7bf0a6f89c2b 100644 --- a/survivor.wdl +++ b/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} }