Make cli-provided module/subworkflow names case insensitive

Uses a click callback function to normalize the name of a module/subworkflow
that is provided by the user on the CLI, so that names written in uppercase
still resolve to the expected lowercase name.

In case no argument is provided, the callback function simply returns None,
and thus the current behaviour of a user being asked to select a component
via an interactive prompt is maintained.

The .casefold() method is used in favour of .lower() for slightly
more robust case normalization.
See: https://stackoverflow.com/questions/45745661/lower-vs-casefold-in-string-matching-and-converting-to-lowercase

The callback is applied to all occurrences of "tool/module/subworkflow" arguments,
except those in the the "create" functions, because these already contain an internal
check that prompts to user to adhere to the lowercase naming convention.

Updates to CHANGELOG.md.

Co-authored-by: Adam Talbot <adam.talbot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Arthur Gymer <24782660+awgymer@users.noreply.github.com>

Author: 4 people

CHANGELOG.md

@@ -41,6 +41,7 @@
 - Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862))
 - Fix schema docs console output truncating ([#2880](https://github.com/nf-core/tools/pull/2880))
 - fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
+- Make cli-provided module/subworkflow names case insensitive ([#2869](https://github.com/nf-core/tools/pull/2869))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 

nf_core/__main__.py

@@ -103,6 +103,14 @@ def selective_traceback_hook(exctype, value, traceback):
 sys.excepthook = selective_traceback_hook
 
 
+# Define callback function to normalize the case of click arguments,
+# which is used to make the module/subworkflow names, provided by the
+# user on the cli, case insensitive.
+def normalize_case(ctx, param, component_name):
+    if component_name is not None:
+        return component_name.casefold()
+
+
 def run_nf_core():
     # print nf-core header if environment variable is not set
     if os.environ.get("_NF_CORE_COMPLETE") is None:
@@ -786,7 +794,7 @@ def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-b
 # nf-core modules install
 @modules.command("install")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -838,7 +846,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha):
 # nf-core modules update
 @modules.command("update")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -930,7 +938,7 @@ def modules_update(
 # nf-core modules patch
 @modules.command()
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -967,7 +975,7 @@ def patch(ctx, tool, dir, remove):
 # nf-core modules remove
 @modules.command("remove")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1121,7 +1129,7 @@ def create_module(
 # nf-core modules test
 @modules.command("test")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1180,7 +1188,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once, profile):
 # nf-core modules lint
 @modules.command("lint")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1267,7 +1275,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
 # nf-core modules info
 @modules.command("info")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1306,7 +1314,7 @@ def modules_info(ctx, tool, dir):
 # nf-core modules bump-versions
 @modules.command()
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1392,7 +1400,7 @@ def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest):
 # nf-core subworkflows test
 @subworkflows.command("test")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1519,7 +1527,7 @@ def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefi
 # nf-core subworkflows lint
 @subworkflows.command("lint")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1600,7 +1608,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
 # nf-core subworkflows info
 @subworkflows.command("info")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="subworkflow name")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1639,7 +1647,7 @@ def subworkflows_info(ctx, tool, dir):
 # nf-core subworkflows install
 @subworkflows.command("install")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1697,7 +1705,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
 # nf-core subworkflows remove
 @subworkflows.command("remove")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1727,7 +1735,7 @@ def subworkflows_remove(ctx, dir, subworkflow):
 # nf-core subworkflows update
 @subworkflows.command("update")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",