Remove samplesheet.wdl

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
-    String? control
-}
-
-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"]
-    }
-}