Merge pull request #93 from rabix/feature/wrabbit-0-2-1

Feature/wrabbit 0 2 1

requirements.txt

@@ -1,6 +1,6 @@
 ruamel.yaml >= 0.16
 sevenbridges-python >= 2.0
 nf-core==2.1
-wrabbit==0.1.3
+wrabbit==0.2.1
 cwlformat
 packaging

sbpack/noncwl/manifest.py

@@ -134,6 +134,8 @@ def validate_sheet(
             continue
         else:
             basename = os.path.basename(path)
+            if not basename:
+                continue
             parent = None
             if os.path.dirname(path):
                 parent = checked[os.path.dirname(path)]
@@ -239,7 +241,7 @@ def main():
         help="Name of the output file.",
     )
     parser.add_argument(
-        "--upload", '-u', action='store_true', required=False,
+        "--upload", action='store_true', required=False,
         help="Upload the file to the project after making it.",
     )
     parser.add_argument(

sbpack/noncwl/nextflow.py

@@ -46,6 +46,9 @@ def nf_schema_build(self):
         Build nextflow schema using nf_core schema build feature and save to
         a file
         """
+        if self.nf_schema_path:
+            return
+
         nf_schema_path = os.path.join(
             self.workflow_path,
             NF_SCHEMA_DEFAULT_NAME,
@@ -64,6 +67,8 @@ def nf_schema_build(self):
         )
         self.nf_schema_path = nf_schema_path
 
+        self.init_config_files()
+
 
 def main():
     # CLI parameters
@@ -248,11 +253,6 @@ def main():
             schema = yaml.safe_load(s)
             nf_wrapper.sb_wrapper.load(schema)
     else:
-        # build schema
-        # Do this only if the nextflow_schema.json is missing
-        if not nf_wrapper.nf_schema_path:
-            nf_wrapper.nf_schema_build()
-
         # Create app
         nf_wrapper.generate_sb_app(
             execution_mode=execution_mode,

sbpack/pack.py

@@ -246,6 +246,15 @@ def resolve_steps(
                     cwl["cwlVersion"] = v["run"]["cwlVersion"]
                     # not really enough, but hope for the best
 
+                if 'sbg:appVersion' not in v["run"]:
+                    v["run"]['sbg:appVersion'] = [cwl.get(
+                        "cwlVersion", cwl_version)]
+                else:
+                    version_ = cwl.get(
+                        "cwlVersion", cwl_version)
+                    if version_ not in v["run"]['sbg:appVersion']:
+                        v["run"]['sbg:appVersion'].append(version_)
+
     return cwl
 
 

sbpack/version.py

@@ -1 +1 @@
-__version__ = "2024.6.3rc1"
+__version__ = "2024.7.11rc1"