nf-core 3.3.2__tar.gz → 3.4.0__tar.gz

{nf_core-3.3.2/nf_core.egg-info → nf_core-3.4.0}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: nf-core
-Version: 3.3.2
+Version: 3.4.0
 Summary: Helper tools for use with nf-core Nextflow pipelines.
 Home-page: https://github.com/nf-core/tools
 Author: Phil Ewels
 Author-email: phil.ewels@scilifelab.se
 License: MIT
 Keywords: nf-core,nextflow,bioinformatics,workflow,pipeline,biology,sequencing,NGS,next generation sequencing
-Requires-Python: >=3.9, <4
+Requires-Python: >=3.10, <4
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click
@@ -20,19 +20,19 @@ Requires-Dist: markdown>=3.3
 Requires-Dist: packaging
 Requires-Dist: pillow
 Requires-Dist: pre-commit
-Requires-Dist: prompt_toolkit<=3.0.51
+Requires-Dist: prompt_toolkit<=3.0.52
 Requires-Dist: pydantic>=2.2.1
 Requires-Dist: pyyaml
 Requires-Dist: questionary>=2.0.1
 Requires-Dist: refgenie
 Requires-Dist: requests
 Requires-Dist: requests_cache
-Requires-Dist: rich-click==1.8.*
+Requires-Dist: rich-click==1.9.*
 Requires-Dist: rich>=13.3.1
 Requires-Dist: rocrate
 Requires-Dist: repo2rocrate
 Requires-Dist: tabulate
-Requires-Dist: textual==3.5.0
+Requires-Dist: textual==6.2.1
 Requires-Dist: trogon
 Requires-Dist: pdiff
 Requires-Dist: ruamel.yaml
@@ -50,8 +50,8 @@ Dynamic: summary
 
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/docs/images/nfcore-tools_logo_dark.png">
-    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/docs/images/nfcore-tools_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png">
+    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_light.png">
   </picture>
 </h1><!-- omit in toc -->
 
@@ -85,7 +85,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.13 nf-core nextflow
+conda create --name nf-core python=3.14 nf-core nextflow
 conda activate nf-core
 ```
 

{nf_core-3.3.2 → nf_core-3.4.0}/README.md

@@ -1,7 +1,7 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/docs/images/nfcore-tools_logo_dark.png">
-    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/docs/images/nfcore-tools_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png">
+    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_light.png">
   </picture>
 </h1><!-- omit in toc -->
 
@@ -35,7 +35,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.13 nf-core nextflow
+conda create --name nf-core python=3.14 nf-core nextflow
 conda activate nf-core
 ```
 

{nf_core-3.3.2 → nf_core-3.4.0}/nf_core/__main__.py

@@ -11,6 +11,7 @@ import rich.console
 import rich.logging
 import rich.traceback
 import rich_click as click
+import rich_click.rich_click as rc
 from trogon import tui
 
 from nf_core import __version__
@@ -59,8 +60,10 @@ from nf_core.commands_test_datasets import (
     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.download.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
@@ -71,51 +74,10 @@ log = logging.getLogger()
 setup_nfcore_dir()
 
 # Set up nicer formatting of click cli help messages
-click.rich_click.MAX_WIDTH = 100
-click.rich_click.USE_RICH_MARKUP = True
-click.rich_click.COMMAND_GROUPS = {
-    "nf-core": [
-        {
-            "name": "Commands",
-            "commands": ["pipelines", "modules", "subworkflows", "test-datasets", "interface"],
-        },
-    ],
-    "nf-core pipelines": [
-        {
-            "name": "For users",
-            "commands": ["list", "launch", "download", "create-params-file"],
-        },
-        {
-            "name": "For developers",
-            "commands": ["create", "lint", "bump-version", "sync", "schema", "rocrate", "create-logo"],
-        },
-    ],
-    "nf-core modules": [
-        {
-            "name": "For pipelines",
-            "commands": ["list", "info", "install", "update", "remove", "patch"],
-        },
-        {
-            "name": "Developing new modules",
-            "commands": ["create", "lint", "test", "bump-versions"],
-        },
-    ],
-    "nf-core subworkflows": [
-        {
-            "name": "For pipelines",
-            "commands": ["list", "info", "install", "update", "remove"],
-        },
-        {
-            "name": "Developing new subworkflows",
-            "commands": ["create", "lint", "test"],
-        },
-    ],
-    "nf-core pipelines schema": [{"name": "Schema commands", "commands": ["validate", "build", "lint", "docs"]}],
-    "nf-core test-datasets": [{"name": "For developers", "commands": ["search", "list", "list-branches"]}],
-}
-click.rich_click.OPTION_GROUPS = {
-    "nf-core modules list local": [{"options": ["--dir", "--json", "--help"]}],
-}
+rc.MAX_WIDTH = 100
+rc.USE_RICH_MARKUP = True
+rc.COMMANDS_BEFORE_OPTIONS = True
+
 
 # Set up rich stderr console
 stderr = rich.console.Console(stderr=True, force_terminal=rich_force_colors())
@@ -147,17 +109,6 @@ def normalize_case(ctx, param, component_name):
         return component_name.casefold()
 
 
-# Define a custom click group class to sort options and commands in the help message
-# TODO: Remove this class and use COMMANDS_BEFORE_OPTIONS when rich-click is updated
-# See https://github.com/ewels/rich-click/issues/200 for more information
-class CustomRichGroup(click.RichGroup):
-    def format_options(self, ctx, formatter) -> None:
-        from rich_click.rich_help_rendering import get_rich_options
-
-        self.format_commands(ctx, formatter)
-        get_rich_options(self, ctx, formatter)
-
-
 def run_nf_core():
     # print nf-core header if environment variable is not set
     if os.environ.get("_NF_CORE_COMPLETE") is None:
@@ -183,11 +134,8 @@ def run_nf_core():
     nf_core_cli(auto_envvar_prefix="NFCORE")
 
 
-@tui(
-    command="interface",
-    help="Launch the nf-core interface",
-)
-@click.group(context_settings=dict(help_option_names=["-h", "--help"]), cls=CustomRichGroup)
+@tui(command="interface", help="Launch the nf-core interface")
+@click.group(context_settings=dict(help_option_names=["-h", "--help"]))
 @click.version_option(__version__)
 @click.option(
     "-v",
@@ -199,6 +147,12 @@ def run_nf_core():
 @click.option("--hide-progress", is_flag=True, default=False, help="Don't show progress bars.")
 @click.option("-l", "--log-file", help="Save a verbose log to a file.", metavar="<filename>")
 @click.pass_context
+@click.rich_config(
+    {
+        "theme": "default-nu",
+        "options_table_column_types": ["opt_long", "opt_short", "help"],
+    }
+)
 def nf_core_cli(ctx, verbose, hide_progress, log_file):
     """
     nf-core/tools provides a set of helper tools for use with nf-core Nextflow pipelines.
@@ -237,7 +191,11 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 
 
 # nf-core pipelines subcommands
-@nf_core_cli.group()
+@nf_core_cli.group(aliases=["p", "pipeline"])
+@click.command_panel("For users", commands=["download", "create-params-file", "launch", "list"])
+@click.command_panel(
+    "For developers", commands=["bump-version", "create", "create-logo", "lint", "rocrate", "schema", "sync"]
+)
 @click.pass_context
 def pipelines(ctx):
     """
@@ -354,7 +312,12 @@ 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",
@@ -393,33 +356,33 @@ def command_pipelines_lint(
 @click.option(
     "-s",
     "--container-system",
-    type=click.Choice(["none", "singularity"]),
+    type=click.Choice(["none", "singularity", "docker"]),
     help="Download container images of required software.",
 )
 @click.option(
     "-l",
     "--container-library",
     multiple=True,
-    help="Container registry/library or mirror to pull images from.",
+    help="Container registry/library or mirror to pull images from. Not available for Docker containers.",
 )
 @click.option(
     "-u",
     "--container-cache-utilisation",
     type=click.Choice(["amend", "copy", "remote"]),
-    help="Utilise a `singularity.cacheDir` in the download process, if applicable.",
+    help="Utilise a `singularity.cacheDir` in the download process, if applicable. Not available for Docker containers.",
 )
 @click.option(
     "-i",
     "--container-cache-index",
     type=str,
-    help="List of images already available in a remote `singularity.cacheDir`.",
+    help="List of images already available in a remote `singularity.cacheDir`. Not available for Docker containers.",
 )
 @click.option(
     "-d",
     "--parallel-downloads",
     type=int,
     default=4,
-    help="Number of parallel image downloads",
+    help="Number of allowed parallel tasks",
 )
 @click.pass_context
 def command_pipelines_download(
@@ -461,7 +424,12 @@ 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 +457,12 @@ 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 +718,12 @@ 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):
     """
@@ -862,7 +840,7 @@ def command_pipelines_schema_docs(directory, schema_file, output, format, force,
 
 
 # nf-core modules subcommands
-@nf_core_cli.group()
+@nf_core_cli.group(aliases=["m", "module"])
 @click.option(
     "-g",
     "--git-remote",
@@ -884,6 +862,8 @@ def command_pipelines_schema_docs(directory, schema_file, output, format, force,
     default=False,
     help="Do not pull in latest changes to local clone of modules repository.",
 )
+@click.command_panel("For pipeline development", commands=["list", "info", "install", "update", "remove", "patch"])
+@click.command_panel("For module development", commands=["create", "lint", "test", "bump-versions"])
 @click.pass_context
 def modules(ctx, git_remote, branch, no_pull):
     """
@@ -944,7 +924,14 @@ 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 +965,14 @@ 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 +1049,14 @@ 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 +1076,14 @@ 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 +1202,14 @@ 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 +1264,14 @@ 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 +1325,14 @@ 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 +1351,14 @@ 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>. Module to bump versions for. If <tool> is provided and <tool/subtool> exists, all subtools will be bumped.",
+    shell_complete=autocomplete_modules,
+)
 @click.option(
     "-d",
     "--dir",
@@ -1333,16 +1369,17 @@ def command_modules_info(ctx, tool, directory):
 )
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
 @click.option("-s", "--show-all", is_flag=True, help="Show up-to-date modules in results too")
-def command_modules_bump_versions(ctx, tool, directory, all, show_all):
+@click.option("-r", "--dry-run", is_flag=True, help="Dry run the command")
+def command_modules_bump_versions(ctx, tool, directory, all, show_all, dry_run):
     """
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
     """
-    modules_bump_versions(ctx, tool, directory, all, show_all)
+    modules_bump_versions(ctx, tool, directory, all, show_all, dry_run)
 
 
 # nf-core subworkflows click command
-@nf_core_cli.group()
+@nf_core_cli.group(aliases=["s", "swf", "subworkflow"])
 @click.option(
     "-g",
     "--git-remote",
@@ -1364,6 +1401,8 @@ def command_modules_bump_versions(ctx, tool, directory, all, show_all):
     default=False,
     help="Do not pull in latest changes to local clone of modules repository.",
 )
+@click.command_panel("For pipeline development", commands=["list", "info", "install", "update", "remove", "patch"])
+@click.command_panel("For module development", commands=["create", "lint", "test", "bump-versions"])
 @click.pass_context
 def subworkflows(ctx, git_remote, branch, no_pull):
     """
@@ -1414,7 +1453,14 @@ 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 +1548,14 @@ 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 +1604,14 @@ 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 +1630,14 @@ 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 +1677,14 @@ 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 +1693,7 @@ 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 +1710,9 @@ 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 +1721,14 @@ 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 +1747,14 @@ 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",
@@ -1750,7 +1838,7 @@ def command_subworkflows_update(
 
 
 # nf-core test-dataset subcommands
-@nf_core_cli.group()
+@nf_core_cli.group(aliases=["tds"])
 @click.pass_context
 def test_datasets(ctx):
     """
@@ -1777,7 +1865,7 @@ def test_datasets(ctx):
     "--generate-dl-url",
     is_flag=True,
     default=False,
-    help="Auto-generate a github url for downloading the test data file based on the branch and query result",
+    help="Auto-generate a github url for downloading the test data file based on the branch and query result. Only applicable when not using -p / --generate-nf-path",
 )
 @click.argument("query", required=False)
 def command_test_dataset_search(ctx, branch, generate_nf_path, generate_dl_url, query):
@@ -1804,7 +1892,7 @@ def command_test_dataset_search(ctx, branch, generate_nf_path, generate_dl_url,
     "--generate-dl-url",
     is_flag=True,
     default=False,
-    help="Auto-generate a github url for downloading the test data file based on the branch and query result",
+    help="Auto-generate a github url for downloading the test data file based on the branch and query result. Only applicable when not using -p / --generate-nf-path",
 )
 def command_test_dataset_list_remote(ctx, branch, generate_nf_path, generate_dl_url):
     """
@@ -2232,7 +2320,7 @@ def command_create_params_file(pipeline, revision, output, force, show_hidden):
 @click.option(
     "-s",
     "--container-system",
-    type=click.Choice(["none", "singularity"]),
+    type=click.Choice(["none", "singularity", "docker"]),
     help="Download container images of required software.",
 )
 @click.option(

{nf_core-3.3.2 → nf_core-3.4.0}/nf_core/commands_modules.py

@@ -183,7 +183,7 @@ def modules_create(
     'modules/local/tool_subtool.nf'
 
     If the specified directory is a clone of nf-core/modules, it creates or modifies files
-    in 'modules/', 'tests/modules' and 'tests/config/pytest_modules.yml'
+    in 'modules/' and 'tests/modules'
     """
     # Combine two bool flags into one variable
     has_meta = None
@@ -334,7 +334,7 @@ def modules_info(ctx, tool, directory):
         sys.exit(1)
 
 
-def modules_bump_versions(ctx, tool, directory, all, show_all):
+def modules_bump_versions(ctx, tool, directory, all, show_all, dry_run):
     """
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
@@ -349,7 +349,7 @@ def modules_bump_versions(ctx, tool, directory, all, show_all):
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
         )
-        version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all)
+        version_bumper.bump_versions(module=tool, all_modules=all, show_up_to_date=show_all, dry_run=dry_run)
     except ModuleExceptionError as e:
         log.error(e)
         sys.exit(1)