udpate yaml config only in pipeline repos

nf-core · Oct 2, 2024 · d0a24be · d0a24be
1 parent a3468d3
commit d0a24be
Showing 1 changed file with 47 additions and 46 deletions.
diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -1136,52 +1136,53 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
             error_message += f"\n{error['loc'][0]}: {error['msg']}"
         raise AssertionError(error_message)
 
-    # Retrieve information if template from config file is empty
-    wf_config = fetch_wf_config(Path(directory))
-    config_template_keys = tools_config["template"].keys() if "template" in tools_config else []
-    if nf_core_yaml_config.template is None:
-        # The .nf-core.yml file did not contain template information
-        nf_core_yaml_config.template = NFCoreTemplateConfig(
-            org="nf-core",
-            name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1],
-            description=wf_config["manifest.description"].strip('"').strip("'"),
-            author=wf_config["manifest.author"].strip('"').strip("'"),
-            version=wf_config["manifest.version"].strip('"').strip("'"),
-            outdir=str(directory),
-            is_nfcore=True,
-        )
-    elif "prefix" in config_template_keys or "skip" in config_template_keys:
-        # The .nf-core.yml file contained the old prefix or skip keys
-        nf_core_yaml_config.template = NFCoreTemplateConfig(
-            org=tools_config["template"]["prefix"]
-            if "prefix" in config_template_keys
-            else tools_config["template"]["org"]
-            if "org" in config_template_keys
-            else "nf-core",
-            name=tools_config["template"]["name"]
-            if "name" in config_template_keys
-            else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1],
-            description=tools_config["template"]["description"]
-            if "description" in config_template_keys
-            else wf_config["manifest.description"].strip('"').strip("'"),
-            author=tools_config["template"]["author"]
-            if "author" in config_template_keys
-            else wf_config["manifest.author"].strip('"').strip("'"),
-            version=tools_config["template"]["version"]
-            if "version" in config_template_keys
-            else wf_config["manifest.version"].strip('"').strip("'"),
-            outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory),
-            skip_features=tools_config["template"]["skip"]
-            if "skip" in config_template_keys
-            else tools_config["template"]["skip_features"]
-            if "skip_features" in config_template_keys
-            else None,
-            is_nfcore=tools_config["template"]["prefix"] == "nf-core"
-            if "prefix" in config_template_keys
-            else tools_config["template"]["org"] == "nf-core"
-            if "org" in config_template_keys
-            else True,
-        )
+    if nf_core_yaml_config["repository_type"] == "pipeline":
+        # Retrieve information if template from config file is empty
+        wf_config = fetch_wf_config(Path(directory))
+        config_template_keys = tools_config["template"].keys() if "template" in tools_config else []
+        if nf_core_yaml_config.template is None:
+            # The .nf-core.yml file did not contain template information
+            nf_core_yaml_config.template = NFCoreTemplateConfig(
+                org="nf-core",
+                name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1],
+                description=wf_config["manifest.description"].strip('"').strip("'"),
+                author=wf_config["manifest.author"].strip('"').strip("'"),
+                version=wf_config["manifest.version"].strip('"').strip("'"),
+                outdir=str(directory),
+                is_nfcore=True,
+            )
+        elif "prefix" in config_template_keys or "skip" in config_template_keys:
+            # The .nf-core.yml file contained the old prefix or skip keys
+            nf_core_yaml_config.template = NFCoreTemplateConfig(
+                org=tools_config["template"]["prefix"]
+                if "prefix" in config_template_keys
+                else tools_config["template"]["org"]
+                if "org" in config_template_keys
+                else "nf-core",
+                name=tools_config["template"]["name"]
+                if "name" in config_template_keys
+                else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1],
+                description=tools_config["template"]["description"]
+                if "description" in config_template_keys
+                else wf_config["manifest.description"].strip('"').strip("'"),
+                author=tools_config["template"]["author"]
+                if "author" in config_template_keys
+                else wf_config["manifest.author"].strip('"').strip("'"),
+                version=tools_config["template"]["version"]
+                if "version" in config_template_keys
+                else wf_config["manifest.version"].strip('"').strip("'"),
+                outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory),
+                skip_features=tools_config["template"]["skip"]
+                if "skip" in config_template_keys
+                else tools_config["template"]["skip_features"]
+                if "skip_features" in config_template_keys
+                else None,
+                is_nfcore=tools_config["template"]["prefix"] == "nf-core"
+                if "prefix" in config_template_keys
+                else tools_config["template"]["org"] == "nf-core"
+                if "org" in config_template_keys
+                else True,
+            )
 
     log.debug("Using config file: %s", config_fn)
     return config_fn, nf_core_yaml_config