Refactor to parse multiple files from the directory

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

nfdocs-parser.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import os
 import yaml
 from docutils import nodes
 from docutils.parsers.rst import Directive
@@ -53,7 +54,22 @@ class NFDocs(Directive):
     def run(self):
         # Take path as single argument for now
         nextflow_path = self.arguments[0]
-        with open(nextflow_path) as nextflow_file:
+        print(nextflow_path)
+
+        # Create dictionaries for each of the block types
+        docstrings = {
+            "process": {},
+            "workflow": {},
+            "function": {}
+        }
+
+        # Create any array to return from the plugin
+        return_nodes = []
+
+        for root, dirs, files in os.walk(nextflow_path):
+            for f in files:
+                if f.endswith(".nf"):
+                    with open(os.path.join(root,f)) as nextflow_file:
 
                         # Split by lines
                         nextflow_lines = nextflow_file.readlines()
@@ -82,13 +98,6 @@ class NFDocs(Directive):
                                     # Add this docstring position to the array
                                     docstring_positions.append(range(doc_start, doc_end+1))
 
-            # Create dictionaries for each of the block types
-            docstrings = {
-                "process": {},
-                "workflow": {},
-                "function": {}
-            }
-
                         # Parse out the docstrings and put them in the appropriate dictionary
                         for pos in docstring_positions:
                             proc_name, proc_type = self.definition_type(nextflow_lines[pos[-1]+1])
@@ -97,9 +106,6 @@ class NFDocs(Directive):
                                 doc_yaml = doc_yaml + nextflow_lines[i].replace(self.DOC_STARTER, "")
                             docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)
 
-            # Create any array to return from the plugin
-            return_nodes = []
-
         # Try to convert each definition to a node
         for block_type, block_docs in docstrings.items():
             block_section = nodes.section()