bug fix

nf_core/__main__.py

@@ -370,9 +370,9 @@ def list(ctx, pipeline_dir, json):
     If no pipeline directory is given, lists all currently available
     software wrappers in the nf-core/modules repository.
     """
-    module_list = nf_core.modules.ModuleList(pipeline_dir)
+    module_list = nf_core.modules.ModuleList(pipeline_dir, json)
     module_list.modules_repo = ctx.obj["modules_repo_obj"]
-    print(module_list.list_modules(json))
+    print(module_list.list_modules())
 
 
 @modules.command(help_priority=2)
@@ -394,7 +394,7 @@ def install(ctx, pipeline_dir, tool, latest, force, sha):
     try:
         module_install = nf_core.modules.ModuleInstall(pipeline_dir, tool, force=force, latest=latest, sha=sha)
         module_install.modules_repo = ctx.obj["modules_repo_obj"]
-        module_install.install(tool)
+        module_install.install()
     except UserWarning as e:
         log.critical(e)
         sys.exit(1)

nf_core/modules/lint.py

@@ -25,7 +25,7 @@
 import sys
 
 import nf_core.utils
-from .pipeline_modules import ModulesRepo
+from .modules_repo import ModulesRepo
 
 log = logging.getLogger(__name__)
 

nf_core/modules/modules_command.py

@@ -22,7 +22,7 @@ def __init__(self, pipeline_dir):
         Initialise the ModulesCommand object
         """
         self.modules_repo = ModulesRepo()
-        self.pipeline_dir = None
+        self.pipeline_dir = pipeline_dir
         self.pipeline_module_names = []
 
     def get_pipeline_modules(self):

nf_core/modules/test_yml_builder.py

@@ -21,7 +21,8 @@
 import operator
 
 import nf_core.utils
-import nf_core.modules.pipeline_modules
+
+from .modules_repo import ModulesRepo
 
 
 log = logging.getLogger(__name__)
@@ -62,7 +63,7 @@ def check_inputs(self):
 
         # Get the tool name if not specified
         if self.module_name is None:
-            modules_repo = nf_core.modules.pipeline_modules.ModulesRepo()
+            modules_repo = ModulesRepo()
             modules_repo.get_modules_file_tree()
             self.module_name = questionary.autocomplete(
                 "Tool name:",