MAINT: Recent CLI tweaks and fixes

beardymcjohnface · Oct 16, 2023 · 2836be2 · 2836be2
1 parent 2d73da4
commit 2836be2
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
@@ -82,7 +82,6 @@ def common_options(func):
             "--snake-default",
             multiple=True,
             default=[
-                "--rerun-incomplete",
                 "--printshellcmds",
                 "--nolock",
                 "--show-failed-logs",
@@ -96,6 +95,11 @@ def common_options(func):
             callback=default_to_output,
             hidden=True,
         ),
+        click.option(
+            "--system-config",
+            default=snake_base(os.path.join("config", "config.yaml")),
+            hidden=True,
+        ),
         click.argument("snake_args", nargs=-1),
     ]
     for option in reversed(options):
@@ -147,27 +151,23 @@ def run(**kwargs):
     """Run {{cookiecutter.project_name}}"""
     # Config to add or update in configfile
     merge_config = {
-        "input": kwargs["_input"],
-        "output": kwargs["output"],
-        "profile": kwargs["profile"],
-        "log": kwargs["log"]
+        "args": kwargs
     }
 
     # run!
     run_snakemake(
         # Full path to Snakefile
         snakefile_path=snake_base(os.path.join("workflow", "Snakefile")),
-        system_config=snake_base(os.path.join("config", "config.yaml")),
         merge_config=merge_config,
         **kwargs
     )
 
 
 @click.command()
 @common_options
-def config(configfile, **kwargs):
+def config(**kwargs):
     """Copy the system default config file"""
-    copy_config(configfile, system_config=snake_base(os.path.join("config", "config.yaml")))
+    copy_config(kwargs["configfile"])
 
 
 @click.command()