Updated nf-core modules remove to remove entry in modules.json

CHANGELOG.md

@@ -20,6 +20,7 @@
 * Use Biocontainers API instead of quayi.io API for `nf-core modules create` [[#875](https://github.com/nf-core/tools/issues/875)]
 * Update `nf-core modules install` to handle different versions of modules  [#1116](https://github.com/nf-core/tools/pull/1116)
 * Refactored `nf-core modules` command into one file per command [#1124](https://github.com/nf-core/tools/pull/1124)
+* Updated `nf-core modules remove` to also remove entry in `modules.json` file ([#1115](https://github.com/nf-core/tools/issues/1115))
 
 #### Sync
 

nf_core/modules/remove.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import json
 import questionary
 import logging
 
@@ -43,7 +44,6 @@ def remove(self, module):
 
         # Set the install folder based on the repository name
         install_folder = ["nf-core", "software"]
-        print(self.modules_repo.name)
         if not self.modules_repo.name == "nf-core/modules":
             install_folder = ["external"]
 
@@ -58,5 +58,27 @@ def remove(self, module):
 
         log.info("Removing {}".format(module))
 
+        # Remove entry from modules.json
+        if not self.remove_modules_json_entry(module):
+            return False
+
         # Remove the module
         return self.clear_module_dir(module_name=module, module_dir=module_dir)
+
+    def remove_modules_json_entry(self, module):
+        # Load 'modules.json'
+        modules_json_path = os.path.join(self.dir, "modules.json")
+        with open(modules_json_path, "r") as fh:
+            modules_json = json.load(fh)
+        if module in modules_json.get("modules", {}):
+            modules_json["modules"].pop(module)
+        else:
+            # If the module is missing from modules.json we can still clear the directory
+            # in which the untracked module resides
+            log.error(f"Module '{module}' is missing from 'modules.json' file.")
+            return questionary.confirm(
+                f"Do you wish to continue removing module '{module}'?", default=False
+            ).unsafe_ask()
+        with open(modules_json_path, "w") as fh:
+            json.dump(modules_json, fh, indent=4)
+        return True