Rework/Add CWL Part

ARC specification.md

@@ -186,21 +186,29 @@ Notes:
 
 Workflow execution and metadata MUST be described using the [Common Workflow Language](https://www.commonwl.org/) (CWL), [v1.2](https://www.commonwl.org/v1.2/) or higher, in a file `workflow.cwl`, which MUST be placed in the subdirectory containing all files specific to this workflow under the top-level `workflows` subdirectory. This file MUST contain either of:
 
-- A CWL [tool description](https://www.commonwl.org/v1.2/CommandLineTool.html). Tool descriptions must be self-contained and not refer to any files outside the workflow subdirectory. All paths used within the tool description MUST be relative to itself.
+- A CWL [tool description](https://www.commonwl.org/v1.2/CommandLineTool.html). Tool descriptions must be self-contained and not refer to any files outside the ARC root directory. All paths used within the tool description MUST be relative to itself.
 
-- A CWL [workflow description](https://www.commonwl.org/v1.2/Workflow.html). Such descriptions MAY utilize other ARC workflows as [nested workflows](https://www.commonwl.org/user_guide/22-nested-workflows/index.html), but MUST use relative paths in this case. Files outside the ARC root directory MUST NOT be referenced.
+- A CWL [workflow description](https://www.commonwl.org/v1.2/Workflow.html). Such descriptions MAY utilize other ARC workflows as [nested workflows](https://www.commonwl.org/user_guide/topics/workflows.html#nested-workflows), but MUST use relative paths in this case. Files outside the ARC root directory MUST NOT be referenced.
 
 Notes:
 
 - There are no requirements on the structure or granularity of workflows. An ARC may contain no workflows at all if it contains no [run results](#run-description), or MAY utilize a single workflow to generate a single run result containing all computational output.
 
 - While workflows typically are (and should be) *generic*, i.e. a single workflow can be applied to different data of the same type, this is not a requirement. It is allowed to hard-code assay file paths and other parameters if workflow reusability is not a priority.
 
-- It is highly recommended that tool descriptions contain a reproducible execution environment description in the form of a [Docker](https://www.commonwl.org/user_guide/07-containers/index.html) container description.
+- It is highly recommended that tool descriptions contain a reproducible execution environment description in the form of a [Docker](https://www.commonwl.org/user_guide/topics/using-containers.html) container description.
 
 - It is expected that workflow and tool descriptions are authored semi-automatically, e.g. using the [arcCommander](https://github.com/nfdi4plants/arcCommander) tool.
 
-- It is strongly encouraged to include author and contributor metadata in tool descriptions and workflow descriptions as [CWL metadata](https://www.commonwl.org/user_guide/17-metadata/index.html).
+### Workflow Metadata
+
+- For metadata annotation, it is encouraged to reference namespaces and schemas, as shown in the [CWL metadata user guide](https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html)
+
+- It is strongly encouraged to include author and contributor metadata in tool descriptions and workflow descriptions as CWL metadata.
+
+    - The referenced authors and contributors must be the ones involved in the creation of the tool description or workflow description, not the person executing the [processing unit](https://www.commonwl.org/user_guide/introduction/basic-concepts.html#processes-and-requirements).
+
+- It is encouraged, to add metadata relevant to the tool description or workflow description. This metadata must be limited to only metadata that directly describes the processing unit. Metadata describing the run parameters must be added to the `run.yml` parameter file.
 
 ## Run Description
 
@@ -218,7 +226,15 @@ Notes:
 
 - It is expected that run descriptions are authored semi-automatically, e.g. using the [arcCommander](https://github.com/nfdi4plants/arcCommander) tool.
 
-- It is strongly encouraged to include author and contributor metadata in run descriptions as [CWL metadata](https://www.commonwl.org/user_guide/17-metadata/index.html).
+### Run Metadata
+
+- For metadata annotation, it is encouraged to reference namespaces and schemas, as shown in the [CWL metadata user guide](https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html)
+
+- It is strongly encouraged to include author and contributor metadata in `run.yml` parameter files as CWL metadata.
+
+ - The referenced authors and contributors must be the ones executing the [processing unit](https://www.commonwl.org/user_guide/introduction/basic-concepts.html#processes-and-requirements), not the person that created the processing unit.
+
+ - It is encouraged, to add metadata relevant to the `run.yml` parameter file. This metadata must be limited to only metadata that directly describes the run parameters. Metadata describing the processing unit must be added to the corresponding `.cwl` file.
 
 ## Additional Payload