add parameter meta

clever.wdl

@@ -23,7 +23,7 @@ task Prediction {
         ~{bwaIndex.fastaFile} \
         ~{outputPath}
     } 
-
+    
     output {
         File predictions = outputPath + "/predictions.vcf"
     }   
@@ -34,6 +34,15 @@ task Prediction {
         docker: dockerImage
     }   
 
+    parameter_meta {
+        bamFile: {description: "The bam file to process.", category: "required"}
+        bamIndex: {description: "The index bam file.", category: "required"}
+        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"}
+        bwaIndex: {description: "The BWA index files.", category: "required"}
+    }
+
 }
 
 task Mateclever {
@@ -76,4 +85,14 @@ task Mateclever {
         memory: memory
         docker: dockerImage 
     }
+
+    parameter_meta {
+        fiteredBam: {description: "The bam file where sequences less than 30bp were removed.", category: "required"}
+        indexedFiteredBam: {description: "The index of the filtered bam file.", category: "required"}
+        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"}
+        bwaIndex: {description: "The BWA index files.", category: "required"}
+        predictions: {description: "The predicted deletions (VCF) from clever.", category: "required"}
+    }
 }

delly.wdl

@@ -30,4 +30,14 @@ task CallSV {
         docker: dockerImage
         memory: memory
     }
+
+    parameter_meta {
+        bamFile: {description: "The bam file to process.", category: "required"}
+        bamIndex: {description: "The index bam file.", category: "required"}
+        referenceFasta: referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
+        referenceFastaFai: { description: "Fasta index (.fai) file of the reference", category: "required" }
+        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"}
+    }
 }

manta.wdl

@@ -116,5 +116,19 @@ task Germline {
         memory: "~{memoryGb}G"
         docker: dockerImage
     }
+
+    parameter_meta {
+        runDir: {description: "The directory to use as run/output directory.", category: "common"}
+        bamFile: {description: "The bam file to process.", category: "required"}
+        bamIndex: {description: "The index bam file.", category: "required"}
+        referenceFasta: referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
+        referenceFastaFai: { description: "Fasta index (.fai) file of the reference", category: "required" }
+        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"}
+        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"}
+    }
 }
     

picard.wdl

@@ -640,5 +640,13 @@ task RenameSample {
         docker: dockerImage
         memory: memory
     }
+
+    parameter_meta {
+        inputVcf: {description: "The VCF file to process.", category: "required"}
+        newSampleName: {description: "A string to replace the old sample name.", category: "required"}
+        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"}
+    }
 }
 

survivor.wdl

@@ -40,4 +40,12 @@ task Merge {
         docker: dockerImage
         memory: memory
     }
+
+    parameter_meta {
+        filePaths: {description: "An array of VCF files (predictions) to be merged by SURVIVOR", category: "required"}
+        sample: {description: "The name of the sample", category: "required"}
+        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"}
+    }
 }