workflow configuration (#157)

* only check for nextflow_schema.json or nextflow.config

* add trailing slash to configurator app url

* ignore interactive validation for output_dir

* handle nextflow schema use of allOf and definitions

---------

Co-authored-by: Lee Pang <[email protected]>

Author: wleepang

cirro/cli/interactive/create_pipeline_config.py

@@ -46,8 +46,7 @@ def ask_output_directory(input_value: str) -> str:
         'type': 'path',
         'name': 'output_dir',
         'message': 'Enter the output directory for the pipeline configuration files',
-        'validate': utils.DirectoryValidator,
-        'default': input_value or '',
+        'default': input_value or str(Path.cwd()),
         'complete_style': CompleteStyle.READLINE_LIKE,
         'only_directories': True
     }

cirro/models/process/nextflow.py

@@ -58,13 +58,15 @@ def get_nextflow_json_schema(workflow_dir: str, logger: Optional[logging.Logger]
             logger.error(msg)
         raise FileNotFoundError(msg)
 
-    _all_of = {}
+    # ignore the 'allOf' attribute if it exists
+    # merge 'definitions' or '$defs' attribute with 'properties'
     if contents.get('allOf'):
-        # this is typically a root attribute in nextflow_schema.json files and a list of $ref
-        # convert this to an object
-        _all_of = {item["$ref"].split('/')[-1]: item for item in contents['allOf']}
         del contents['allOf']
 
-    contents['properties'] = contents.get('properties', {}) | _all_of
+    contents['properties'] = (
+        contents.get('properties', {})
+        | contents.get('$defs', {})
+        | contents.get('definitions', {})
+    )
 
     return contents

cirro/models/process/process.py

@@ -8,7 +8,7 @@
 from referencing import Resource, Registry
 
 
-CONFIG_APP_URL = "https://app.cirro.bio/tools/pipeline-configurator"
+CONFIG_APP_URL = "https://app.cirro.bio/tools/pipeline-configurator/"
 
 
 class ConfigAppStatus(Enum):
@@ -51,7 +51,7 @@ def parameter_schema(self) -> Resource:
             # look for a nextflow_schema.json file at the root of the workflow directory
             is_nextflow = (
                 ('nextflow_schema.json' in filenames)
-                or ('main.nf' in filenames and 'nextflow.config' in filenames)
+                or ('nextflow.config' in filenames)
             )
             if is_nextflow:
                 # lazy load nextflow dependencies