Merge pull request #37 from biowdl/BIOWDL-19

Add samplesheet structs

samplesheet.wdl

+version 1.0
+struct Readgroup {
+    String id
+    File R1
+    String R1_md5
+    File? R2
+    String R2_md5
+}
+
+struct Library {
+    String id
+    Array[Readgroup]+ readgroups
+}
+
+struct Sample {
+    String id
+    Array[Library]+ libraries
+}
+
+task sampleConfigFileToStruct {
+    input {
+        File sampleConfigFile
+        String outputJson = "output.json"
+    }
+
+    # Below command can convert any samplesheet with a nested dictionary
+    # structure to a list of objects model.
+    # It was specifically designed to run on both python2 and python3.
+    # Only requirement is PyYAML.
+    #
+    # Code maintained in https://github.com/rhpvorderman/samplesheet-to-struct
+    # can be moved to biowdl group later.
+    command {
+        python <<CODE
+
+        import yaml
+        import json
+
+
+        def nested_dicts_to_lists(dictionary):
+            new_dict = dict()
+            for key, value in dictionary.items():
+                if type(value) == dict:
+                    new_dict[key] = dict_to_item_list_with_id(value)
+                else:
+                    new_dict[key] = value
+            return new_dict
+
+
+        def dict_to_item_list_with_id(dictionary):
+            items = []
+            for sub_key, sub_dictionary in dictionary.items():
+                item_dict = dict(id=sub_key, **nested_dicts_to_lists(sub_dictionary))
+                items.append(item_dict)
+            return items
+
+
+        with open("~{sampleConfigFile}", "r") as samplesheet:
+            samplesheet_dict = yaml.load(samplesheet)
+
+        sample_struct = nested_dicts_to_lists(samplesheet_dict)
+
+        with open("~{outputJson}", "w") as output_json:
+            output_json.write(json.dumps(sample_struct))
+
+        CODE
+    }
+
+    output {
+        Map[String,Array[Sample]] map = read_json(outputJson)
+        Array[Sample] samples = map["samples"]
+     }
+}
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