From 67bfc3a52caa427d85c98f7a79676c14b8059c59 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Tue, 17 Oct 2023 10:12:43 +1030
Subject: [PATCH] BUG: misc fixes

---
 tests/test_snaketool.py                                    | 2 +-
 {{cookiecutter.project_slug}}/setup.py                     | 2 +-
 .../{{cookiecutter.project_slug}}/__main__.py              | 6 +++---
 .../{{cookiecutter.project_slug}}/config/config.yaml       | 7 ++++---
 .../{{cookiecutter.project_slug}}/workflow/Snakefile       | 1 -
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/test_snaketool.py b/tests/test_snaketool.py
index 452a52d..3eb540f 100644
--- a/tests/test_snaketool.py
+++ b/tests/test_snaketool.py
@@ -46,6 +46,6 @@ def test_snaketool_cli(tmp_dir):
 
 def test_snaketool_commands(tmp_dir):
     """test Snaketool"""
-    exec_command("my_snaketool run --input yeet")
+    exec_command("my_snaketool run --input yeet --no-use-conda ")
     exec_command("my_snaketool config")
     exec_command("my_snaketool citation")
diff --git a/{{cookiecutter.project_slug}}/setup.py b/{{cookiecutter.project_slug}}/setup.py
index 0104237..6df83bd 100644
--- a/{{cookiecutter.project_slug}}/setup.py
+++ b/{{cookiecutter.project_slug}}/setup.py
@@ -52,7 +52,7 @@ def get_data_files():
     data_files=get_data_files(),
     py_modules=["{{cookiecutter.project_slug}}"],
     install_requires=[
-        "snaketool-utils>=0.0.3",
+        "snaketool-utils>=0.0.4",
         "snakemake{{cookiecutter.snakemake_version}}",
         "pyyaml{{cookiecutter.pyyaml_version}}",
         "Click{{cookiecutter.click_version}}",
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
index c34e174..041e756 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
@@ -151,7 +151,7 @@ def run(**kwargs):
     """Run {{cookiecutter.project_name}}"""
     # Config to add or update in configfile
     merge_config = {
-        "{{cookiecutter.project_name}}": {
+        "{{cookiecutter.project_slug}}": {
             "args": kwargs
         }
     }
@@ -167,9 +167,9 @@ def run(**kwargs):
 
 @click.command()
 @common_options
-def config(**kwargs):
+def config(configfile, system_config, **kwargs):
     """Copy the system default config file"""
-    copy_config(kwargs["configfile"])
+    copy_config(configfile, system_config=system_config)
 
 
 @click.command()
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
index c7d157f..5c2a172 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
@@ -1,5 +1,6 @@
 # Namespaced config file example
 {{cookiecutter.project_slug}}:
-    args:
-        # Command line args will overwrite anything here at runtime
-    # Customisable config here
+    args: # Command line args will be (over)written here at runtime
+        input:
+        output:
+    # Add customisable config here
\ No newline at end of file
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
index 6dad1ee..8067bc2 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
@@ -2,7 +2,6 @@
 # Update default config with runtime config
 configfile: os.path.join(workflow.basedir, "../", "config", "config.yaml")
 configfile: os.path.join(workflow.basedir, "../", "config", "system_config.yaml")
-config.update(config["{{cookiecutter.project_slug}}"]) # convenience if using namespaced config
 
 
 # Rules files