Merge pull request #2 from maxibor/main

Switch skeleton to cookiecutter

.github/workflows/linting.yml

@@ -1,6 +1,5 @@
-name: nf-core linting
+name: markdown linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
 on:
   push:
   pull_request:

.gitignore

@@ -42,6 +42,146 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+
 ######################
 ## PROJECT SPECIFIC ##
 ######################

README.md

@@ -1,6 +1,6 @@
-# Opinionated Bioinformatics Project Directory Structure
+# Cookiecutter opinionated bioinformatics project structure
 
-![Version Badge](https://img.shields.io/badge/Version-1.0.1-brightgreen?style=for-the-badge)
+![Version Badge](https://img.shields.io/badge/Version-1.0.2-brightgreen?style=for-the-badge)
 
 ## Table of Contents
 
@@ -20,6 +20,16 @@ To ensure reproducibility and readability within bioinformatics projects, we pro
 
 This structure has been developed out of (meta)genomics projects, however it should be generic enough for other fields to adopt.
 
+## How to install
+
+To use this bioinformatics project skeleton, you will need to use [Cookiecutter](https://cookiecutter.readthedocs.io/en/1.7.2/first_steps.html). Head over to the [Cookiecutter documentation for installation instructions](https://cookiecutter.readthedocs.io/en/1.7.2/installation.html), we recommend you to use conda.
+
+Once Cookiecutter is installed, it's just a matter of:  
+
+```bash
+cookiecutter https://github.com/paleobiotechnology/analysis-project-structure
+```
+
 ## General Organisation
 
 The three main concepts for this structure is as follows:

cookiecutter.json

@@ -0,0 +1,6 @@
+{
+    "project_name": "MyCoolPaleoBiotechnologyProject",
+    "project_description": "This is a project about cool data with nicely documented analysis",
+    "authors": "John Doe",
+    "version": "1.0.2"
+}

{{cookiecutter.project_name}}/01-documentation/README.md

@@ -0,0 +1,3 @@
+# This is the documentation of {{cookiecutter.project_name}}
+
+You can use the [Markdown syntax](https://www.markdownguide.org/basic-syntax/)  to organize your documentation.

{{cookiecutter.project_name}}/02-scripts/README.md

@@ -0,0 +1,5 @@
+# This directory contains the scripts used in the {{cookiecutter.project_name}} project
+
+**TODO**: Please list your scripts and described what they do
+
+You can use the [Markdown syntax](https://www.markdownguide.org/basic-syntax/)  to organize your documentation.

{{cookiecutter.project_name}}/05-results/README.md

@@ -0,0 +1,5 @@
+# This directory contains the results of {{cookiecutter.project_name}} project
+
+**TODO**: Please list your results and described what they are
+
+You can use the [Markdown syntax](https://www.markdownguide.org/basic-syntax/)  to organize your documentation.

{{cookiecutter.project_name}}/README.md

@@ -0,0 +1,11 @@
+# {{cookiecutter.project_name}}
+
+![Version Badge](https://img.shields.io/badge/Version-{{cookiecutter.version}}-brightgreen?style=for-the-badge)
+
+## Introduction
+
+{{cookiecutter.project_description}}
+
+## Authors
+
+{{cookiecutter.authors}}

conda_environment.yml → {{cookiecutter.project_name}}/conda_environment.yml

@@ -1,7 +1,7 @@
 
 ## You can use this file, or make multiple files, to create a conda environment for this project:
 ##   conda env create -f environment.yml
-name: NAME_OF_PROJECT_UPDATE_ME
+name: {{cookiecutter.project_name}}
 channels:
   - conda-forge
   - bioconda