nf-core · LouisLeNezet · Jul 15, 2025 · Jul 7, 2025 · Jul 7, 2025 · Jul 8, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -54,6 +54,7 @@
 - Update error message for rocrate_readme_sync ([#3652](https://github.com/nf-core/tools/pull/3652))
 - Update `nf-core modules info` command after `meta.yml` restructuring ([#3659](https://github.com/nf-core/tools/pull/3659))
 - Enable parsing of multi-line config values ([#3629](https://github.com/nf-core/tools/pull/3629))
+- Add modules / subworkflows and pipelines names autocompletion to the CLI ([#3660](https://github.com/nf-core/tools/pull/3660))
 
 #### Version updates
 

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -59,8 +59,10 @@
     test_datasets_list_remote,
     test_datasets_search,
 )
+from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows
 from nf_core.components.constants import NF_CORE_MODULES_REMOTE
 from nf_core.pipelines.download import DownloadError
+from nf_core.pipelines.list import autocomplete_pipelines
 from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
 
 # Set up logging as the root logger
@@ -354,7 +356,12 @@ def command_pipelines_lint(
 
 # nf-core pipelines download
 @pipelines.command("download")
-@click.argument("pipeline", required=False, metavar="<pipeline name>")
+@click.argument(
+    "pipeline",
+    required=False,
+    metavar="<pipeline name>",
+    shell_complete=autocomplete_pipelines,
+)
 @click.option(
     "-r",
     "--revision",
@@ -461,7 +468,12 @@ def command_pipelines_download(
 
 # nf-core pipelines create-params-file
 @pipelines.command("create-params-file")
-@click.argument("pipeline", required=False, metavar="<pipeline name>")
+@click.argument(
+    "pipeline",
+    required=False,
+    metavar="<pipeline name>",
+    shell_complete=autocomplete_pipelines,
+)
 @click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)")
 @click.option(
     "-o",
@@ -489,7 +501,12 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force,
 
 # nf-core pipelines launch
 @pipelines.command("launch")
-@click.argument("pipeline", required=False, metavar="<pipeline name>")
+@click.argument(
+    "pipeline",
+    required=False,
+    metavar="<pipeline name>",
+    shell_complete=autocomplete_pipelines,
+)
 @click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)")
 @click.option("-i", "--id", help="ID for web-gui launch parameter set")
 @click.option(
@@ -745,7 +762,12 @@ def pipeline_schema():
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-@click.argument("pipeline", required=True, metavar="<pipeline name>")
+@click.argument(
+    "pipeline",
+    required=False,
+    metavar="<pipeline name>",
+    shell_complete=autocomplete_pipelines,
+)
 @click.argument("params", type=click.Path(exists=True), required=True, metavar="<JSON params file>")
 def command_pipelines_schema_validate(directory, pipeline, params):
     """
@@ -944,7 +966,14 @@ def command_modules_list_local(ctx, keywords, json, directory):  # pylint: disab
 # nf-core modules install
 @modules.command("install")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -978,7 +1007,14 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha):
 # nf-core modules update
 @modules.command("update")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1055,7 +1091,14 @@ def command_modules_update(
 # nf-core modules patch
 @modules.command("patch")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1075,7 +1118,14 @@ def command_modules_patch(ctx, tool, directory, remove):
 # nf-core modules remove
 @modules.command("remove")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1194,7 +1244,14 @@ def command_modules_create(
 # nf-core modules test
 @modules.command("test")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-v",
     "--verbose",
@@ -1249,7 +1306,14 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
 # nf-core modules lint
 @modules.command("lint")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1303,7 +1367,14 @@ def command_modules_lint(
 # nf-core modules info
 @modules.command("info")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1322,7 +1393,14 @@ def command_modules_info(ctx, tool, directory):
 # nf-core modules bump-versions
 @modules.command("bump-versions")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1414,7 +1492,14 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force, migr
 # nf-core subworkflows test
 @subworkflows.command("test")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1502,7 +1587,14 @@ def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint:
 # nf-core subworkflows lint
 @subworkflows.command("lint")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1551,7 +1643,14 @@ def command_subworkflows_lint(
 # nf-core subworkflows info
 @subworkflows.command("info")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1570,7 +1669,14 @@ def command_subworkflows_info(ctx, subworkflow, directory):
 # nf-core subworkflows install
 @subworkflows.command("install")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1610,7 +1716,14 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha
 # nf-core subworkflows patch
 @subworkflows.command("patch")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1619,7 +1732,7 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option("-r", "--remove", is_flag=True, default=False, help="Remove an existent patch file and regenerate it.")
-def subworkflows_patch(ctx, tool, dir, remove):
+def subworkflows_patch(ctx, subworkflow, dir, remove):
     """
     Create a patch file for minor changes in a subworkflow
 
@@ -1636,9 +1749,9 @@ def subworkflows_patch(ctx, tool, dir, remove):
             ctx.obj["modules_repo_no_pull"],
         )
         if remove:
-            subworkflow_patch.remove(tool)
+            subworkflow_patch.remove(subworkflow)
         else:
-            subworkflow_patch.patch(tool)
+            subworkflow_patch.patch(subworkflow)
     except (UserWarning, LookupError) as e:
         log.error(e)
         sys.exit(1)
@@ -1647,7 +1760,14 @@ def subworkflows_patch(ctx, tool, dir, remove):
 # nf-core subworkflows remove
 @subworkflows.command("remove")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1666,7 +1786,14 @@ def command_subworkflows_remove(ctx, directory, subworkflow):
 # nf-core subworkflows update
 @subworkflows.command("update")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+    shell_complete=autocomplete_subworkflows,
+)
 @click.option(
     "-d",
     "--dir",

diff --git a/nf_core/components/components_completion.py b/nf_core/components/components_completion.py
@@ -0,0 +1,37 @@
+import sys
+
+from click.shell_completion import CompletionItem
+
+from nf_core.modules.list import ModuleList
+from nf_core.subworkflows.list import SubworkflowList
+
+
+def autocomplete_components(ctx, param, incomplete: str, component_type: str, list_class):
+    # Defaults
+    modules_repo_url = "https://github.com/nf-core/modules"
+    modules_repo_branch = "master"
+    modules_repo_no_pull = False
+    dir_folder = ctx.params.get("dir", ".")
+
+    try:
+        if ctx.obj is not None:
+            modules_repo_url = ctx.obj.get("modules_repo_url", modules_repo_url)
+            modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch)
+            modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull)
+
+        components_list = list_class(dir_folder, True, modules_repo_url, modules_repo_branch, modules_repo_no_pull)
+
+        available_components = components_list.modules_repo.get_avail_components(component_type)
+
+        return [CompletionItem(comp) for comp in available_components if comp.startswith(incomplete)]
+    except Exception as e:
+        print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr)
+        return []
+
+
+def autocomplete_modules(ctx, param, incomplete: str):
+    return autocomplete_components(ctx, param, incomplete, "modules", ModuleList)
+
+
+def autocomplete_subworkflows(ctx, param, incomplete: str):
+    return autocomplete_components(ctx, param, incomplete, "subworkflows", SubworkflowList)