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Add aliases to sub-subcommands like install, lint, etc. #3980

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Add aliases to sub-subcommands like install, lint, etc. #3980

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6702e76
add aliases to more commands
mashehu Jan 12, 2026
750b79f
[automated] Update CHANGELOG.md
nf-core-bot Jan 12, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@

- fix test for linting for version.yml ([#3947](https://github.com/nf-core/tools/pull/3947))
- more fixes for incorrect parsing of version statement ([#3973](https://github.com/nf-core/tools/pull/3973))
- Add aliases to common sub-subcommands like `install`, `lint`, etc. ([#3980](https://github.com/nf-core/tools/pull/3980))

### Modules

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44 changes: 22 additions & 22 deletions nf_core/__main__.py
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Expand Up @@ -203,7 +203,7 @@ def pipelines(ctx):


# nf-core pipelines create
@pipelines.command("create")
@pipelines.command("create", aliases=["c"])
@click.pass_context
@click.option(
"-n",
Expand Down Expand Up @@ -231,7 +231,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out


# nf-core pipelines lint
@pipelines.command("lint")
@pipelines.command("lint", aliases=["l"])
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -307,7 +307,7 @@ def command_pipelines_lint(


# nf-core pipelines download
@pipelines.command("download")
@pipelines.command("download", aliases=["d"])
@click.argument(
"pipeline",
required=False,
Expand Down Expand Up @@ -522,7 +522,7 @@ def command_pipelines_launch(


# nf-core pipelines list
@pipelines.command("list")
@pipelines.command("list", aliases=["ls"])
@click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
@click.option(
"-s",
Expand Down Expand Up @@ -625,7 +625,7 @@ def command_pipelines_sync(


# nf-core pipelines bump-version
@pipelines.command("bump-version")
@pipelines.command("bump-version", aliases=["bump", "bv", "b"])
@click.pass_context
@click.argument("new_version", required=True, metavar="<new version>")
@click.option(
Expand Down Expand Up @@ -769,7 +769,7 @@ def command_pipelines_schema_build(directory, no_prompts, web_only, url):


# nf-core pipelines schema lint
@pipeline_schema.command("lint")
@pipeline_schema.command("lint", aliases=["l"])
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -879,7 +879,7 @@ def modules(ctx, git_remote, branch, no_pull):


# nf-core modules list subcommands
@modules.group("list")
@modules.group("list", aliases=["ls"])
@click.pass_context
def modules_list(ctx):
"""
Expand Down Expand Up @@ -921,7 +921,7 @@ def command_modules_list_local(ctx, keywords, json, directory): # pylint: disab


# nf-core modules install
@modules.command("install")
@modules.command("install", aliases=["add", "i"])
@click.pass_context
@click.argument(
"tool",
Expand Down Expand Up @@ -962,7 +962,7 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha):


# nf-core modules update
@modules.command("update")
@modules.command("update", aliases=["up", "u"])
@click.pass_context
@click.argument(
"tool",
Expand Down Expand Up @@ -1073,7 +1073,7 @@ def command_modules_patch(ctx, tool, directory, remove):


# nf-core modules remove
@modules.command("remove")
@modules.command("remove", aliases=["uninstall", "rm", "r"])
@click.pass_context
@click.argument(
"tool",
Expand All @@ -1099,7 +1099,7 @@ def command_modules_remove(ctx, directory, tool):


# nf-core modules create
@modules.command("create")
@modules.command("create", aliases=["c"])
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="<directory>")
Expand Down Expand Up @@ -1199,7 +1199,7 @@ def command_modules_create(


# nf-core modules test
@modules.command("test")
@modules.command("test", aliases=["t"])
@click.pass_context
@click.argument(
"tool",
Expand Down Expand Up @@ -1261,7 +1261,7 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile


# nf-core modules lint
@modules.command("lint")
@modules.command("lint", aliases=["l"])
@click.pass_context
@click.argument(
"tool",
Expand Down Expand Up @@ -1348,7 +1348,7 @@ def command_modules_info(ctx, tool, directory):


# nf-core modules bump-versions
@modules.command("bump-versions")
@modules.command("bump-versions", aliases=["bump-version", "bump", "bv", "b"])
@click.pass_context
@click.argument(
"tool",
Expand Down Expand Up @@ -1418,7 +1418,7 @@ def subworkflows(ctx, git_remote, branch, no_pull):


# nf-core subworkflows create
@subworkflows.command("create")
@subworkflows.command("create", aliases=["c"])
@click.pass_context
@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="<directory>")
Expand Down Expand Up @@ -1450,7 +1450,7 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force, migr


# nf-core subworkflows test
@subworkflows.command("test")
@subworkflows.command("test", aliases=["t"])
@click.pass_context
@click.argument(
"subworkflow",
Expand Down Expand Up @@ -1503,7 +1503,7 @@ def command_subworkflows_test(ctx, subworkflow, directory, no_prompts, update, o


# nf-core subworkflows list subcommands
@subworkflows.group("list")
@subworkflows.group("list", aliases=["ls"])
@click.pass_context
def subworkflows_list(ctx):
"""
Expand Down Expand Up @@ -1545,7 +1545,7 @@ def command_subworkflows_list_local(ctx, keywords, json, directory): # pylint:


# nf-core subworkflows lint
@subworkflows.command("lint")
@subworkflows.command("lint", aliases=["l"])
@click.pass_context
@click.argument(
"subworkflow",
Expand Down Expand Up @@ -1627,7 +1627,7 @@ def command_subworkflows_info(ctx, subworkflow, directory):


# nf-core subworkflows install
@subworkflows.command("install")
@subworkflows.command("install", aliases=["add", "i"])
@click.pass_context
@click.argument(
"subworkflow",
Expand Down Expand Up @@ -1718,7 +1718,7 @@ def subworkflows_patch(ctx, subworkflow, dir, remove):


# nf-core subworkflows remove
@subworkflows.command("remove")
@subworkflows.command("remove", aliases=["uninstall", "rm", "r"])
@click.pass_context
@click.argument(
"subworkflow",
Expand All @@ -1744,7 +1744,7 @@ def command_subworkflows_remove(ctx, directory, subworkflow):


# nf-core subworkflows update
@subworkflows.command("update")
@subworkflows.command("update", aliases=["up", "u"])
@click.pass_context
@click.argument(
"subworkflow",
Expand Down Expand Up @@ -1876,7 +1876,7 @@ def command_test_dataset_search(ctx, branch, generate_nf_path, generate_dl_url,


# nf-core test-dataset search
@test_datasets.command("list")
@test_datasets.command("list", aliases=["ls"])
@click.pass_context
@click.option("-b", "--branch", type=str, help="Branch in the test-datasets repository to reduce search to")
@click.option(
Expand Down