add default outputPath

bcftools.wdl

@@ -25,7 +25,7 @@ version 1.0
 task Bcf2Vcf {
     input {
         File bcf
-        String outputPath
+        String outputPath = "./bcftools/SV.vcf"
         String dockerImage = "quay.io/biocontainers/bcftools:1.9--ha228f0b_3"
     }
 

clever.wdl

@@ -30,7 +30,7 @@ task Mateclever {
         File indexedFiteredBam
         BwaIndex bwaIndex
         File predictions
-        String outputPath
+        String outputPath = "./clever"
         Int cleverMaxDelLength = 100000
         Int maxLengthDiff= 30
         Int maxOffset = 150
@@ -84,7 +84,7 @@ task Prediction {
         File bamFile
         File bamIndex
         BwaIndex bwaIndex
-        String outputPath
+        String outputPath = "./clever"
 
         Int threads = 10
         String memory = "15G"

delly.wdl

@@ -28,7 +28,7 @@ task CallSV {
         File bamIndex
         File referenceFasta
         File referenceFastaFai
-        String outputPath
+        String outputPath = "./delly/delly.vcf"
 
         String memory = "15G"
         String dockerImage = "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"

manta.wdl

@@ -26,7 +26,7 @@ task Germline {
         File bamIndex
         File referenceFasta
         File referenceFastaFai
-        String runDir
+        String runDir = "./manta_run"
         File? callRegions
         File? callRegionsIndex
         Boolean exome = false

picard.wdl

@@ -642,9 +642,8 @@ task SortVcf {
 task RenameSample {
     input {
         File inputVcf
-        String outputPath
+        String outputPath = "./picard/renamed.vcf"
         String newSampleName
-
         String memory = "24G"
         String javaXmx = "8G"
         String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"

survivor.wdl

@@ -31,7 +31,7 @@ task Merge {
         Int strandType = 1
         Int distanceBySvSize = 0
         Int minSize = 30
-        String outputPath
+        String outputPath = "./survivor/merged.vcf"
         String memory = "24G"
         String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
     }