From 2836be25b12a578ac40886fcde54c6c57578ab10 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Mon, 16 Oct 2023 16:30:26 +1030
Subject: [PATCH] MAINT: Recent CLI tweaks and fixes

---
 .../{{cookiecutter.project_slug}}/__main__.py    | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
index 8bc1918..6fe6745 100644
--- 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):
@@ -147,17 +151,13 @@ 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
     )
@@ -165,9 +165,9 @@ def run(**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()