Merge pull request #6 from rabix/feature/publishDir_support

Binding takes itemSeparator and shellQuote

wrabbit/parser/constants.py

@@ -66,17 +66,19 @@ class EXTENSIONS:
 }
 
 GENERIC_NF_OUTPUT_DIRECTORY = {
-    "id": "nf_workdir",
+    "id": "nf_publishdir",
     "type": [
         'null',
-        'Directory'
+        {
+            'type': 'array',
+            'items': 'File'
+        }
     ],
-    "label": "Work Directory",
+    "label": "Publish Directory",
     "doc": "This is a template output. "
-           "Please change glob to directories specified in "
-           "publishDir in the workflow.",
+           "You can modify the glob pattern to make outputs more specific.",
     "outputBinding": {
-        'glob': "work"
+        'glob': "*"
     }
 }
 
@@ -139,6 +141,7 @@ def sample_sheet(
 SB_SCHEMA_DEFAULT_NAME = 'sb_nextflow_schema'
 README_DEFAULT_NAME = 'README.md'
 MINIMUM_SUPPORTED_NF_VERSION = "21.10.0"
+NFCORE_OUTPUT_DIRECTORY_ID = 'outdir'
 
 # Mappings of nextflow input fields to SB input fields
 #  nextflow_key: cwl_key mapping

wrabbit/parser/nextflow.py

@@ -34,6 +34,7 @@
     SAMPLE_SHEET_SWITCH,
     LOAD_LISTING_REQUIREMENT,
     SKIP_NEXTFLOW_TOWER_KEYS,
+    NFCORE_OUTPUT_DIRECTORY_ID,
 )
 
 from wrabbit.specification.node import (
@@ -60,6 +61,11 @@
 
 
 class NextflowParser:
+    nf_config_files: list
+    nf_schema_path: Optional[str]
+    readme_path: Optional[str]
+    sb_samplesheet_schema: Optional[str]
+
     def __init__(
             self, workflow_path: str,
             sb_doc: Optional[str] = None,
@@ -72,7 +78,7 @@ def __init__(
         self.workflow_path = workflow_path
 
         # Locate nextflow files in the package if possible
-        self.nf_config_files = get_config_files(self.workflow_path) or []
+        self.init_config_files()
         self.nf_schema_path = get_nf_schema(self.workflow_path)
         self.readme_path = get_docs_file(self.workflow_path)
         self.sb_samplesheet_schema = get_sample_sheet_schema(
@@ -85,6 +91,13 @@ def __init__(
         self.executor_version = executor_version
         self.sb_package_id = sb_package_id
 
+    def init_config_files(self):
+        """
+        Config may be initialized multiple times while working with a code
+        package in case a new config file is generated with nf-core lib.
+        """
+        self.nf_config_files = get_config_files(self.workflow_path) or []
+
     def generate_sb_inputs(self):
         """
         Generate SB inputs schema
@@ -159,6 +172,12 @@ def generate_sb_inputs(self):
                         required=req,
                     ))
 
+        # Remap publishDir to string type
+        if temp := self.sb_wrapper.get_input(NFCORE_OUTPUT_DIRECTORY_ID):
+            print(f"Detected publishDir input --{temp.id_}. Remapping to "
+                  f"string type input.")
+            temp.set_property('type', 'string')
+
         # Add the generic file array input - auxiliary files
         self.sb_wrapper.safe_add_input(GENERIC_FILE_ARRAY_INPUT)
         self.sb_wrapper.safe_add_input(NF_PARAMS_FILE_INPUT)
@@ -210,12 +229,13 @@ def generate_app_data(self):
                 # Stop searching if manifest is found
                 break
 
-        self.executor_version = self.executor_version or \
-                                get_executor_version(self.sb_doc)
+        if not self.executor_version and self.sb_doc:
+            self.executor_version = get_executor_version(self.sb_doc)
 
-        # Confirm if the executor version is valid.
-        # If it is below 22.10.1 it is not supported.
-        self.executor_version.correct_version()
+        if self.executor_version:
+            # Confirm if the executor version is valid.
+            # If it is below 22.10.1 it is not supported.
+            self.executor_version.correct_version()
 
         # step2: add links
 

wrabbit/parser/utils.py

@@ -226,7 +226,7 @@ def get_nf_schema(string):
     if os.path.exists(path):
         return path
     else:
-        raise Exception()
+        return None
 
 
 def get_docs_file(path):

wrabbit/specification/binding.py

@@ -10,8 +10,10 @@ def __init__(
             **kwargs
     ):
         self.prefix = prefix
-        self.item_separator = item_separator
-        self.shell_quote = shell_quote
+        self.item_separator = item_separator or \
+            kwargs.get('itemSeparator', None)
+        self.shell_quote = shell_quote or \
+            kwargs.get('shellQuote', None)
         self.glob = glob
 
     def serialize(self):

wrabbit/specification/listing.py

@@ -35,3 +35,8 @@ def deserialize(listing):
         elif isinstance(listing, str):
             return Listing(listing)
         return Listing(**listing)
+
+    def __eq__(self, other):
+        assert isinstance(other, Listing)
+
+        return self.__dict__ == other.__dict__

wrabbit/specification/requirements.py

@@ -37,8 +37,10 @@ def add_listing(self, obj: Union[dict, str, Listing]):
         if not self.listing:
             self.listing = list()
 
-        if obj not in self.listing:
-            self.listing.append(obj)
+        for ref_obj in self.listing:
+            if ref_obj != obj:
+                self.listing.append(obj)
+                break
 
     def serialize(self):
         temp = {

wrabbit/version.py

@@ -1 +1 @@
-__version__ = "0.1.3"
+__version__ = "0.2.0"

wrabbit/wrapper/wrapper.py

@@ -128,6 +128,7 @@ def add_requirement(self, requirement: [dict, Requirement]):
         for req in self.requirements:
             if req.class_ == requirement.class_:
                 req.update(requirement)
+                break
         else:
             # add new class
             self.requirements.append(requirement)