Add method to store params

CHANGELOG.md

@@ -11,6 +11,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Added
 - Functional testing framework with concrete tests for `methods.set_env()`
 - Functional test for `bam_parser.parse_bam_header()`.
+- Dump parameters with `json_extractor.store_params_json()`
 
 ---
 

config/store_object_as_json/README.md

@@ -0,0 +1,24 @@
+# Storage of map-like objects into JSON 
+
+This module takes an arbritrary map-like object and a `File`, and converts the object into JSON and saves it into
+the path-specified by `File`.
+
+## Example
+
+Shown is an example to store the `params` object into as a JSON file into the log folder.
+
+Example:
+```Nextflow
+includeConfig "/path/to/store_object_as_json.config"
+...
+methods {
+    ...
+    setup = {
+        ...
+        json_extractor.store_object_as_json(
+            params, // object to be stored
+            new File("${params.log_output_dir}/params.json")
+        )
+    }
+}
+```

config/store_object_as_json/store_object_as_json.config

@@ -0,0 +1,12 @@
+import groovy.json.JsonOutput
+
+json_extractor {
+    store_object_as_json = { Map object, File destination ->
+        json_object = JsonOutput.prettyPrint(JsonOutput.toJson(object))
+        File parent = destination.getParentFile()
+        if (!parent.exists()) {
+            parent.mkdirs()
+            }
+        destination.write(json_object)
+      }
+ }