Created wdls to extract filter values into json

wdl/ExtractFiltersFromVcfs.wdl

@@ -0,0 +1,100 @@
+version 1.0
+
+workflow ExtractFiltersFromVCFs {
+
+  input {
+    Array[File] vcf_files
+
+    String sv_pipeline_docker
+  }
+
+  scatter (vcf in vcf_files) {
+    call ExtractSampleAndVariants { 
+			input:
+				vcf_file = vcf, 
+				sv_pipeline_docker = sv_pipeline_docker
+    }
+  }
+
+  call MergeJSONs {
+    input: 
+			json_files = ExtractSampleAndVariants.output_json,
+			sv_pipeline_docker = sv_pipeline_docker
+  }
+
+  output {
+    File filters_json = MergeJSONs.merged_json
+  }
+}
+
+task ExtractSampleAndVariants {
+  input {
+    File vcf_file
+    String sv_pipeline_docker
+  }
+
+  command <<<
+    set -e
+
+    sample_id=$(bcftools query -l ~{vcf_file} | head -n 1)
+
+    output_json="${sample_id}.json"
+    echo "{ \"$sample_id\": {" > "$output_json"
+
+    bcftools query -f '%ID\t%FILTER\n' ~{vcf_file} | \
+    awk -v sample="$sample_id" '
+    BEGIN { first=1 }
+    {
+      if ($2 != "PASS") {
+        gsub(":", "_", $1);
+        if (!seen[$2]) {
+          if (!first) print ",";
+          first=0;
+          printf "\"%s\": [\"%s\"]", $2, $1;
+          seen[$2]=1;
+        } else {
+          printf ", \"%s\"", $1;
+        }
+      }
+    }
+    END { print "}}" }' >> "$output_json"
+  >>>
+
+  output {
+    File output_json = "~{vcf_file}.json"
+  }
+
+  runtime {
+    docker: sv_pipeline_docker
+  }
+}
+
+task MergeJSONs {
+  input {
+    Array[File] json_files
+
+		String sv_pipeline_docker
+  }
+
+  command <<<
+    set -e
+    echo "{" > merged.json
+
+    first=1
+    for f in ~{sep=' ' json_files}; do
+      if [[ "$first" -eq 0 ]]; then echo "," >> merged.json; fi
+      cat "$f" | jq -c . >> merged.json
+      first=0
+    done
+
+    echo "}" >> merged.json
+  >>>
+
+  output {
+    File merged_json = "merged.json"
+  }
+
+	runtime {
+    docker: sv_pipeline_docker
+  }
+}