Project readme

mccoy/main.py

@@ -35,6 +35,8 @@ def create_project(project_name, reference: Path, xml_template: Path, copy_workf
     shutil.copyfile(mccoy_dir / "tests.py", project_dir / "tests.py")
     (project_dir / 'runs').mkdir()
 
+    shutil.copyfile(mccoy_dir / "readme_template.md", project_dir / "README.md")
+
 
 def get_last_run_id(project_path):
     runs = [int(run.split("_")[-1]) for run in glob(f"{project_path}/runs/*") if Path(run).is_dir()]

mccoy/readme_template.md

@@ -0,0 +1,44 @@
+```
+  __  __       _____
+ |  \/  |     / ____|
+ | \  / | ___| |     ___  _   _
+ | |\/| |/ __| |    / _ \| | | |
+ | |  | | (__| |___| (_) | |_| |
+ |_|  |_|\___|\_____\___/ \__, |
+                           __/ |
+                          |___/ 
+```
+
+This project was created with the [McCoy](https://github.com/mccoy-devs/mccoy) CLI.
+
+
+# Project layout
+
+Here you will find the following files and directories:
+
+1. `config.yaml`: The configuration file for this project. You can use
+   this to change the command line arguments and options for your runs. See the
+   docs for more information.
+
+2. `tests.py`: [Phytest](https://github.com/phytest-devs/phytest) quality
+   control checks that will be run as part of the pipeline. This will also
+   need to be adapted to suit your particular usecase and needs.
+
+3. `resources`: This directory contains the reference sequence and BEAST2
+   template which was provided during project creation.
+
+4. `runs`: This is where each run of McCoy will be stored (see below).
+
+
+# Running McCoy
+
+To run McCoy from within this directory:
+
+```
+mccoy run . --data <PATH TO YOUR FASTA FILE>
+```
+
+To see a list of other options which can be passed to McCoy, run
+`mccoy run --help`. Any unrecognised arguments will be forwarded on to
+Snakemake. A full list of possible snakemake arguments can be found
+by running `mccoy run --help-snakemake`.

mccoy/workflow/Snakefile

@@ -15,10 +15,11 @@ SCRIPT_DIR = SNAKE_DIR / "scripts"
 # overwrite config with project specific file
 configfile: Path(config['project_path']) / "config.yaml"
 
+
 # use the config file to update our default resources
 if extra := config["all"].get("update_default_resources", None):
-  for k, v in extra.items():
-    workflow.default_resources.set_resource(k, v)
+    for k, v in extra.items():
+        workflow.default_resources.set_resource(k, v)
 
 # Ensure log directory exists. Required for cluster job submission.
 # TODO(SM): Not sure if this is needed now with the slurm profile...