update parameters meta

clever.wdl

@@ -41,6 +41,8 @@ task Prediction {
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
                       category: "advanced"}
         bwaIndex: {description: "The BWA index files.", category: "required"}
+        memory: {description: "The memory required to run the programs", category: "common"}
+        threads: {description: "The the number of threads required to run a program", category: "common"}
     }
 
 }
@@ -94,5 +96,7 @@ task Mateclever {
                       category: "advanced"}
         bwaIndex: {description: "The BWA index files.", category: "required"}
         predictions: {description: "The predicted deletions (VCF) from clever.", category: "required"}
+        memory: {description: "The memory required to run the programs", category: "common"}
+        threads: {description: "The the number of threads required to run a program", category: "common"}
     }
 }

delly.wdl

@@ -39,5 +39,6 @@ task CallSV {
         outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
                       category: "advanced"}
+        memory: {description: "The memory required to run the programs", category: "common"}
     }
 }

manta.wdl

@@ -128,6 +128,8 @@ task Germline {
         callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
         callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
         exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
+        memoryGb: {description: "The memory required to run the manta", category: "common"}
+        cores: {description: "The the number of cores required to run a program", category: "common"}
     }
 }
     

picard.wdl

@@ -647,6 +647,8 @@ task RenameSample {
         outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
                       category: "advanced"}
+        javaXmx: {description: "The max. memory allocated for JAVA", category: "common"}
+        memory: {description: "The memory required to run the programs", category: "common"}
     }
 }
 

survivor.wdl

@@ -47,5 +47,12 @@ task Merge {
         outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
                       category: "advanced"}
+        minSize: {description: "The mimimum size of SV to be merged", category: "required"}
+        distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "required"}
+        strandType: {description: "A boolean to include strand type of an SV to be merged", category: "required"}
+        svType: {description: "A boolean to include the type SV to be merged", category: "required"}
+        suppVecs: {description: "The minimum number of SV callers to support the merging", category: "required"}
+        breakpointDistance: {description: "The distance between pairwise breakpoints between SVs", category: "required"}
+        memory: {description: "The memory required to run the programs", category: "common"}
     }
 }