Sequana Pipeline Template

Version:	2.0

This repository is a Cookiecutter template to start a new Sequana pipeline implementation from scratch.

Quickstart

You first need to install the latest version of cookiecutter if you haven't installed it yet (requires Cookiecutter 1.4.0 or higher):

pip install -U cookiecutter

Then, no need to install the sequana_pipeline_template package itself. You can call it directly from github as follows:

cookiecutter https://github.com/sequana/sequana_pipeline_template.git

you will be asked some questions in particular the name of the package. You can change things later on. Except the name, most entries are populated in the setup.py file.

• The first question asks the name of the future pipeline. There is no strict

convention in Sequana but we usually use small caps and underscores to separate words (e.g., sequana_rnaseq).

• The second question is the short description that will be added to your

setup.py configuration file

• The third questions asked for keywords, also added to the setup.py

That's it.

If your pipeline is called varseq, you should end up with a structure in the directory sequana_varseq similar to

similar to

├── test
│   └── __init__.py
├── doc
│   ├── conf.py
│   ├── index.rst
│   └── Makefile
├── README.rst
├── requirements.txt
├── sequana_pipelines
│   └── varseq
│       ├── config.yaml
│       ├── __init__.py
│       ├── main.py
│       ├── varseq.rules
│       ├── README.rst
│       ├── requirements.txt
│       └── schema.yaml
│       └── data
│           ├── __init__.py
├── setup.cfg
└── setup.py

You can install this new pipeline as follows:

cd sequana_varseq
python setup.py install

You can build the documentation as follows:

cd sequana_varseq/doc
make html  # under linux

Or test it:

cd sequana_varseq
pytest  # this tool (pytest) must be install first (pip install pytest)

Of course, you now need to work a little bit by replacing the content of some files with your code and/or documentation and tests.

The most important editing steps are then:

1. to edit the config.yaml and varseq.rules in the sequana_pipelines/varseq directory with your own snakemake pipeline and configuration file.
2. edit the main script main.py and adapt it to your needs. This will be the entry point of the user.
3. the documentation in ./doc
4. test in ./test
5. update the requirements.txt file in varseq/ directory to add any external dependencies. The requirements.txt at the top level is only for Python dependencies. In principle it depends only on sequana

Once done, create a repository on https://github.com/sequana/sequana_varseq and upload your files.

This is not perfect and we will most probably edit this template in the future to make it more robust and possibly add such features (help needed).

Once happy, you can create a local repository:

git init

Create and switch to main branch: if you are on a different branch, you can create and switch to the main branch with:

git checkout -b main

Add and commit changes: ensure you have at least one commit in your repository. Make an initial commit:

git add .
git commit -m "Initial commit"

Push to Remote Repository: try pushing to the remote repository:

git remote add origin git@github.com:sequana/your_repo
git push -u origin main

Changelog

• v2: uses poetry
• v1: uses setuptools