From d9c0f67a825a5b618c1ea2ec3da40f0c26ea85f7 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Wed, 28 Jun 2023 13:46:45 +0930
Subject: [PATCH 1/9] DEV: Can now double-handle --profile e.g. to pass to
 config for use in sub-workflows

---
 {{cookiecutter.project_slug}}/setup.py           |  2 +-
 .../{{cookiecutter.project_slug}}/__main__.py    | 16 +++++++++++-----
 .../config/config.yaml                           |  1 +
 3 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/setup.py b/{{cookiecutter.project_slug}}/setup.py
index 27cf368..0104237 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>=0.0.2",
+        "snaketool-utils>=0.0.3",
         "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 5e0f462..8bc1918 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
@@ -59,6 +59,12 @@ def common_options(func):
         click.option(
             "--threads", help="Number of threads to use", default=1, show_default=True
         ),
+        click.option(
+            "--profile",
+            default=None,
+            help="Snakemake profile to use",
+            show_default=False,
+        ),
         click.option(
             "--use-conda/--no-use-conda",
             default=True,
@@ -137,13 +143,14 @@ def cli():
 )
 @click.option("--input", "_input", help="Input file/directory", type=str, required=True)
 @common_options
-def run(_input, output, log, **kwargs):
+def run(**kwargs):
     """Run {{cookiecutter.project_name}}"""
     # Config to add or update in configfile
     merge_config = {
-        "input": _input,
-        "output": output,
-        "log": log
+        "input": kwargs["_input"],
+        "output": kwargs["output"],
+        "profile": kwargs["profile"],
+        "log": kwargs["log"]
     }
 
     # run!
@@ -152,7 +159,6 @@ def run(_input, output, log, **kwargs):
         snakefile_path=snake_base(os.path.join("workflow", "Snakefile")),
         system_config=snake_base(os.path.join("config", "config.yaml")),
         merge_config=merge_config,
-        log=log,
         **kwargs
     )
 
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
index c5b84ef..1284e8d 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
@@ -1,4 +1,5 @@
 # Snakemake config
 input:
 output: '{{cookiecutter.project_slug}}.out/'
+profile:
 log: '{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}.log'
\ No newline at end of file

From 903c115cd8e5b6b6fbe2dd11b6ec51d2daac3f0f Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Mon, 16 Oct 2023 16:00:37 +1030
Subject: [PATCH 2/9] DEV: Update to include more thorough file structure for
 convenience

---
 tests/test_snaketool.py                       |  3 +-
 .../config/config.yaml                        | 10 ++---
 .../config/system_config.yaml                 |  2 +
 .../workflow/Snakefile                        | 43 ++++---------------
 .../workflow/envs/example.yaml                |  5 +++
 .../workflow/rules/example.smk                | 11 +++++
 .../workflow/rules/preflight.smk              | 43 +++++++++++++++++++
 .../workflow/scripts/example.py               |  7 +++
 8 files changed, 84 insertions(+), 40 deletions(-)
 create mode 100644 {{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/system_config.yaml
 create mode 100644 {{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/envs/example.yaml
 create mode 100644 {{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk
 create mode 100644 {{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk
 create mode 100644 {{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/scripts/example.py

diff --git a/tests/test_snaketool.py b/tests/test_snaketool.py
index acd78a3..452a52d 100644
--- a/tests/test_snaketool.py
+++ b/tests/test_snaketool.py
@@ -41,10 +41,11 @@ def test_snaketool_cli(tmp_dir):
     exec_command("my_snaketool -h")
     exec_command("my_snaketool run -h")
     exec_command("my_snaketool config -h")
+    exec_command("my_snaketool --version")
 
 
 def test_snaketool_commands(tmp_dir):
     """test Snaketool"""
     exec_command("my_snaketool run --input yeet")
     exec_command("my_snaketool config")
-    exec_command("my_snaketool citation")
\ No newline at end of file
+    exec_command("my_snaketool citation")
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
index 1284e8d..c7d157f 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/config.yaml
@@ -1,5 +1,5 @@
-# Snakemake config
-input:
-output: '{{cookiecutter.project_slug}}.out/'
-profile:
-log: '{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}.log'
\ No newline at end of file
+# Namespaced config file example
+{{cookiecutter.project_slug}}:
+    args:
+        # Command line args will overwrite anything here at runtime
+    # Customisable config here
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/system_config.yaml b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/system_config.yaml
new file mode 100644
index 0000000..d7ccea4
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/config/system_config.yaml
@@ -0,0 +1,2 @@
+{{cookiecutter.project_slug}}:
+    # Config you don't want users to change
\ 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 4d1b588..6dad1ee 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
@@ -1,40 +1,20 @@
-import glob
 
+# 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
 
-configfile: os.path.join(workflow.basedir, '../', 'config', 'config.yaml')
 
-
-# Concatenate Snakemake's own log file with the master log file
-def copy_log_file():
-    files = glob.glob(os.path.join(".snakemake", "log", "*.snakemake.log"))
-    if not files:
-        return None
-    current_log = max(files, key=os.path.getmtime)
-    shell("cat " + current_log + " >> " + config['log'])
-
-onsuccess:
-    copy_log_file()
-
-onerror:
-    copy_log_file()
-
-
-# Target file
-outTouch = os.path.join(config['output'], config['input'])
-
-
-# Mark target rules
-target_rules = []
-def targetRule(fn):
-    assert fn.__name__.startswith('__')
-    target_rules.append(fn.__name__[2:])
-    return fn
+# Rules files
+include: os.path.join(workflow.basedir, "rules", "preflight.smk")
+include: os.path.join(workflow.basedir, "rules", "example.smk")
 
 
+# Target rules
 @targetRule
 rule all:
     input:
-        outTouch
+        targets
 
 
 @targetRule
@@ -42,8 +22,3 @@ rule print_targets:
     run:
         print("\nTop level rules are: \n", file=sys.stderr)
         print("* " + "\n* ".join(target_rules) + "\n\n", file=sys.stderr)
-
-
-rule yeet:
-    output:
-        touch(outTouch)
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/envs/example.yaml b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/envs/example.yaml
new file mode 100644
index 0000000..3bf8ab1
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/envs/example.yaml
@@ -0,0 +1,5 @@
+name: python
+channels:
+    - defaults
+dependencies:
+    - python>=3.9
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk
new file mode 100644
index 0000000..dd16bc7
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk
@@ -0,0 +1,11 @@
+rule example:
+    output:
+        os.path.join(dirs["result"], "example.done")
+    conda:
+        os.path.join(dirs["envs"], "example.yaml")
+    benchmark:
+        os.path.join(dirs["bench"], "example.txt")
+    log:
+        os.path.join(dirs["logs"], "example.err")
+    script:
+        os.path.join(dirs["scripts"], "example.py")
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk
new file mode 100644
index 0000000..3302d6a
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk
@@ -0,0 +1,43 @@
+
+# Directories
+dirs = {
+    "logs": os.path.join(config["output"], "logs"),
+    "bench": os.path.join(config["output"], "bench"),
+    "results": os.path.join(config["output"], "results"),
+    "envs": os.path.join(workflow.basedir, "envs"),
+    "scripts": os.path.join(workflow.basedir, "scripts")
+}
+
+
+# Targets
+targets = [
+    os.path.join(dirs["results"], "example.done")
+]
+
+
+# Misc
+target_rules = []
+
+
+def targetRule(fn):
+    """Mark rules as target rules for rule print_targets"""
+    assert fn.__name__.startswith("__")
+    target_rules.append(fn.__name__[2:])
+    return fn
+
+
+def copy_log_file():
+    """Concatenate Snakemake log to output log file"""
+    import glob
+
+    files = glob.glob(os.path.join(".snakemake", "log", "*.snakemake.log"))
+    if files:
+        current_log = max(files, key=os.path.getmtime)
+        shell("cat " + current_log + " >> " + config["args"]["log"])
+
+
+onsuccess:
+    copy_log_file()
+
+onerror:
+    copy_log_file()
diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/scripts/example.py b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/scripts/example.py
new file mode 100644
index 0000000..6a3560e
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/scripts/example.py
@@ -0,0 +1,7 @@
+
+def main(**kwargs):
+    open(kwargs["output"], "w").close()
+
+
+if __name__ == "__main__":
+    main(output=snakemake.output[0],)

From 43ca23c2a0d3d89c9216361ccb9e3c7c6ec8bb95 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Mon, 16 Oct 2023 16:17:22 +1030
Subject: [PATCH 3/9] BUG: fix example

---
 .../{{cookiecutter.project_slug}}/workflow/rules/example.smk    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk
index dd16bc7..65fb085 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/example.smk
@@ -1,6 +1,6 @@
 rule example:
     output:
-        os.path.join(dirs["result"], "example.done")
+        os.path.join(dirs["results"], "example.done")
     conda:
         os.path.join(dirs["envs"], "example.yaml")
     benchmark:

From 2d73da4082cd9f0da7fef31d9f38d68c15f455c7 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Mon, 16 Oct 2023 16:17:39 +1030
Subject: [PATCH 4/9] MAINT: don't ddos codecov

---
 .github/workflows/codecov.yml    | 69 ++++++++++++++++++++++++++++++++
 .github/workflows/python-app.yml |  9 +----
 2 files changed, 70 insertions(+), 8 deletions(-)
 create mode 100644 .github/workflows/codecov.yml

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
new file mode 100644
index 0000000..e3bba8d
--- /dev/null
+++ b/.github/workflows/codecov.yml
@@ -0,0 +1,69 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Codecov
+
+on:
+  push:
+    branches: [ "main" ]
+    paths:
+      - '.github/**'
+      - 'build/**'
+      - 'tests/**'
+      - '{{cookiecutter.project_slug}}/**'
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - '.github/**'
+      - 'build/**'
+      - 'tests/**'
+      - '{{cookiecutter.project_slug}}/**'
+
+permissions:
+  contents: read
+
+jobs:
+  tests:
+    name: "Codecov using python ${{ matrix.python-version }} on ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.10"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+        with:
+          fetch-depth: 0
+
+      # Setup env
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: snaketool
+          environment-file: build/environment.yaml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: "Setup Snaketool on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          cookiecutter --no-input ./
+          cd my_snaketool/
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=./ --cov-report=xml --cov-append
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: true
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index abbeaf0..d2079d7 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -24,7 +24,7 @@ permissions:
 
 jobs:
   tests:
-    name: "Python ${{ matrix.python-version }}"
+    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
 
     defaults:
@@ -60,10 +60,3 @@ jobs:
         run: |
           pip install pytest pytest-cov
           pytest --cov=./ --cov-report=xml --cov-append
-          
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          file: coverage.xml
-          fail_ci_if_error: true

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 5/9] 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()

From b8ef89925b92a5e8e8ed332ed0776da38f210091 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Mon, 16 Oct 2023 16:36:58 +1030
Subject: [PATCH 6/9] BUG: config fixes

---
 .../workflow/rules/preflight.smk                            | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk
index 3302d6a..8b720ee 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/rules/preflight.smk
@@ -1,9 +1,9 @@
 
 # Directories
 dirs = {
-    "logs": os.path.join(config["output"], "logs"),
-    "bench": os.path.join(config["output"], "bench"),
-    "results": os.path.join(config["output"], "results"),
+    "logs": os.path.join(config["args"]["output"], "logs"),
+    "bench": os.path.join(config["args"]["output"], "bench"),
+    "results": os.path.join(config["args"]["output"], "results"),
     "envs": os.path.join(workflow.basedir, "envs"),
     "scripts": os.path.join(workflow.basedir, "scripts")
 }

From 7f1077cbcedd582ad3cf0f6e70f9ca7d370dc31a Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Mon, 16 Oct 2023 16:50:16 +1030
Subject: [PATCH 7/9] BUG: config fixes

---
 .../{{cookiecutter.project_slug}}/__main__.py                 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
index 6fe6745..c34e174 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py
@@ -151,7 +151,9 @@ def run(**kwargs):
     """Run {{cookiecutter.project_name}}"""
     # Config to add or update in configfile
     merge_config = {
-        "args": kwargs
+        "{{cookiecutter.project_name}}": {
+            "args": kwargs
+        }
     }
 
     # run!

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 8/9] 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

From 98079c7cbdab76b50cfd9d71aa07055c4d1ca963 Mon Sep 17 00:00:00 2001
From: Michael Roach <beardymcjohnface@gmail.com>
Date: Tue, 17 Oct 2023 10:25:23 +1030
Subject: [PATCH 9/9] BUG: misc fix

---
 .../{{cookiecutter.project_slug}}/workflow/Snakefile             | 1 +
 1 file changed, 1 insertion(+)

diff --git a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
index 8067bc2..6dad1ee 100644
--- a/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
+++ b/{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/workflow/Snakefile
@@ -2,6 +2,7 @@
 # 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