keep error when no subworkflows installed but allow it when linting a…

… pipeline

nf_core/__main__.py

@@ -613,7 +613,10 @@ def lint(
             json,
             ctx.obj["hide_progress"],
         )
-        if len(lint_obj.failed) + len(module_lint_obj.failed) + len(subworkflow_lint_obj.failed) > 0:
+        swf_failed = 0
+        if subworkflow_lint_obj is not None:
+            swf_failed = len(subworkflow_lint_obj.failed)
+        if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)

nf_core/components/lint/__init__.py

@@ -97,7 +97,9 @@ def __init__(
                         )
                     )
             if not self.all_remote_components:
-                log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
+                raise LookupError(
+                    f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
+                )
             local_component_dir = Path(self.dir, self.component_type, "local")
             self.all_local_components = []
             if local_component_dir.exists():

nf_core/lint/__init__.py

@@ -91,7 +91,10 @@ def run_linting(
     # Create the modules lint object
     module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
     # Create the subworkflows lint object
-    subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
+    try:
+        subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
+    except LookupError:
+        subworkflow_lint_obj = None
 
     # Verify that the pipeline is correctly configured and has  a modules.json file
     module_lint_obj.has_valid_directory()
@@ -114,7 +117,8 @@ def run_linting(
         module_lint_tests = ("module_changes", "module_version")
         subworkflow_lint_tests = ("subworkflow_changes", "subworkflow_version")
     module_lint_obj.filter_tests_by_key(module_lint_tests)
-    subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
 
     # Set up files for modules linting test
     module_lint_obj.set_up_pipeline_files()
@@ -133,15 +137,17 @@ def run_linting(
     if len(module_lint_obj.all_remote_components) > 0:
         module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
     # Run the subworkflows lint tests
-    if len(subworkflow_lint_obj.all_local_components) > 0:
-        subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
-    if len(subworkflow_lint_obj.all_remote_components) > 0:
-        subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
+    if subworkflow_lint_obj is not None:
+        if len(subworkflow_lint_obj.all_local_components) > 0:
+            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
+        if len(subworkflow_lint_obj.all_remote_components) > 0:
+            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
 
     # Print the results
     lint_obj._print_results(show_passed)
     module_lint_obj._print_results(show_passed, sort_by=sort_by)
-    subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
     nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
     nf_core.lint_utils.print_fixes(lint_obj)
 

nf_core/lint_utils.py

@@ -18,11 +18,18 @@
 
 def print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj):
     """Print a joint summary of the general pipe lint tests and the module and subworkflow lint tests"""
-    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + len(subworkflow_lint_obj.passed)
+    swf_passed = 0
+    swf_warned = 0
+    swf_failed = 0
+    if subworkflow_lint_obj is not None:
+        swf_passed = len(subworkflow_lint_obj.passed)
+        swf_warned = len(subworkflow_lint_obj.warned)
+        swf_failed = len(subworkflow_lint_obj.failed)
+    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + swf_passed
     nbr_ignored = len(lint_obj.ignored)
     nbr_fixed = len(lint_obj.fixed)
-    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + len(subworkflow_lint_obj.warned)
-    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + len(subworkflow_lint_obj.failed)
+    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + swf_warned
+    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed
 
     summary_colour = "red" if nbr_failed > 0 else "green"
     table = Table(box=rich.box.ROUNDED, style=summary_colour)