From d230e3ff252184807990af97ad61c3e1adddeb5b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 25 Jul 2018 12:10:48 +0200
Subject: [PATCH] add samplesheet
---
samplesheet.wdl | 66 +++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 66 insertions(+)
create mode 100644 samplesheet.wdl
diff --git a/samplesheet.wdl b/samplesheet.wdl
new file mode 100644
index 0000000..a33131c
--- /dev/null
+++ b/samplesheet.wdl
@@ -0,0 +1,66 @@
+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"
+ }
+
+ command {
+ python3 <<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"]
+ }
+}
\ No newline at end of file
--
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