From 2b592518cb5abbd1825ae310aa9e6d67ad8af18e Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Thu, 9 Aug 2018 11:34:01 +0200
Subject: [PATCH] Remove samplesheet.wdl
---
samplesheet.wdl | 75 -------------------------------------------------
1 file changed, 75 deletions(-)
delete mode 100644 samplesheet.wdl
diff --git a/samplesheet.wdl b/samplesheet.wdl
deleted file mode 100644
index d036f4d..0000000
--- a/samplesheet.wdl
+++ /dev/null
@@ -1,75 +0,0 @@
-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"]
- }
-}
--
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