add SV task: clever.wdl

clever.wdl

+version 1.0 
+
+import "common.wdl"
+import "bwa.wdl"
+task Prediction {
+    input {
+        IndexedBamFile bamFile
+        BwaIndex bwaIndex
+        String outputPath        
+        Int threads = 10 
+    }   
+    
+
+    command <<< 
+        set -e
+        mkdir -p $(dirname ~{outputPath})
+        clever \
+        -T ~{threads} \
+        --use_mapq \
+        --sorted \
+        -f \
+        ~{bamFile.file} \
+        ~{bwaIndex.fastaFile} \
+        ~{outputPath}
+    >>> 
+
+    output {
+        File predictions = "~{outputPath}/predictions.vcf"
+    }   
+    
+    runtime {
+        cpu: threads
+        docker: "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
+    }   
+
+}
+
+task Mateclever {
+    input {
+        IndexedBamFile bamFile
+        BwaIndex bwaIndex
+        File predictions
+        String outputPath
+        Int threads = 10 
+        Int cleverMaxDelLength = 100000
+        Int maxLengthDiff= 30
+        Int maxOffset = 150 
+    }
+
+    command <<<
+        set -e
+        mkdir -p $(dirname ~{outputPath})
+        echo ~{outputPath} ~{bamFile.file} ~{predictions} none > predictions.list
+        mateclever \
+        -T ~{threads} \
+        -k \
+        -f \
+        -M ~{cleverMaxDelLength} \
+        -z ~{maxLengthDiff} \
+        -o ~{maxOffset} \
+        ~{bwaIndex.fastaFile} \
+        predictions.list \
+        ~{outputPath}
+    >>>
+    
+    output {
+        File matecleverVcf = "~{outputPath}/deletions.vcf" 
+    }
+    
+    runtime {
+        cpu: threads
+        docker: "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
+    }
+}