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my-snaketool

Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff

https://github.com/beardymcjohnface/snaketool

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.4%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff

Basic Info
  • Host: GitHub
  • Owner: beardymcjohnface
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 74.2 KB
Statistics
  • Stars: 49
  • Watchers: 1
  • Forks: 3
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

Snaketool

GitHub last commit CI

Cookiecutter profile for making a Snakemake-based bioinformatics tool.

See Nektool for a NextFlow-based template

Motivation

Writing reliable command line tools requires a lot of boilerplate to ensure input and generated files are valid, catch errors with subprocesses, log stderr messages etc. It's very time-consuming and annoying. Snakemake does a lot of heavy lifting in this regard and is an obvious alternative to a command line tool.

While Snakemake pipelines are excellent, cloning a pipeline repo every time you want to run an analysis is also annoying. So too is manually punching in the full path to a Snakefile somewhere on your system, as well as copying and manually updating the config file for your analysis.

Building a Snakemake pipeline with a convenience launcher offers the best of both worlds: - Developing command line applications is quicker and easier - Installing, running, and rerunning is easier and more convenient - You can have subcommands for utility scripts and Snakefiles - You can trick NextFlow users into running Snakemake - Your pipelines have help messages!

Who is this for?

People who are already familiar with Snakemake and want to create either a Snakemake-powered commandline tool or make their pipelines fancier and more user-friendly.

Citation

This template is published in Plos Computational Biology:

https://doi.org/10.1371/journal.pcbi.1010705

Usage

Install Cookiecutter if you don't already have it.

shell conda create -n cookiecutter -c conda-forge cookiecutter conda activate cookiecutter

Download the template with Cookiecutter and follow the prompts

shell cookiecutter https://github.com/beardymcjohnface/Snaketool.git

And here's what you get:

```text mysnaketool/ ├── MANIFEST.in ├── mysnaketool │   ├── config │   │   ├── config.yaml │   │   └── systemconfig.yaml │   ├── _init.py │   ├── __main.py │   ├── mysnaketool.CITATION │   ├── mysnaketool.LICENSE │   ├── my_snaketool.VERSION │   └── workflow │   ├── envs │   │   └── example.yaml │   ├── rules │   │   ├── example.smk │   │   └── preflight.smk │   ├── scripts │   │   └── example.py │   └── Snakefile ├── README.md └── setup.py

```

The file __main__.py is the entry point. Once installed with pip it will be accessible on command line, in this example as my_snaketool. Customise this file to add your own commandline options, help message etc. If you only have one Snakefile you wish to run then this file will need very little customisation. If you're happy only using --input and --output you don't have to do anything!

The directories config/ and workflow/ contain an example Snakemake pipeline that will work with the example launcher.

How the launcher works

The launcher first copies the default config file to the working directory which will allow the user to cusomise their config if they wish. The launcher reads in this config file and combines it with command-line arguments. In this example it only has two config-related options to pass: --input and --output. The Launcher updates the config file with these options before passing it to Snakemake.
Most of the other command line arguments are boilerplate for running Snakemake and do not require much if any customisation.

Customising your tool

Check out the wiki page for a detailed example on customising your Snaketool.

Installing and testing your tool

For development, cd to your Snaketool directory and install with pip:

shell cd snaketool/ pip install -e . my_snaketool --help my_snaketool run --help

Test run the template:

shell my_snaketool run --input yeet

Publishing your tool

Check out the wiki page for a detailed look at publishing your tool to PyPI and Conda

Owner

  • Name: Michael Roach
  • Login: beardymcjohnface
  • Kind: user
  • Company: Flinders University

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Roach"
    given-names: "Michael J"
    orcid: "https://orcid.org/0000-0003-1488-5148"
  - family-names: "Pierce-Ward"
    given-names: "N Tessa"
    orcid: "https://orcid.org/0000-0002-2942-5331"
  - family-names: "Suchecki"
    given-names: "Radoslaw"
    orcid: "https://orcid.org/0000-0003-4992-9497"
  - family-names: "Mallawaarachchi"
    given-names: "Vijini"
    orcid: "https://orcid.org/0000-0002-2651-8719"
  - family-names: "Papudeshi"
    given-names: "Bhavya"
    orcid: "https://orcid.org/0000-0001-5359-3100"
  - family-names: "Handley"
    given-names: "Scott A"
    orcid: "https://orcid.org/0000-0002-2143-6570"
  - family-names: "Brown"
    given-names: "C Titus"
    orcid: "https://orcid.org/0000-0001-6001-2677"
  - family-names: "Watson-Haigh"
    given-names: "Nathan S"
    orcid: "https://orcid.org/0000-0002-7935-6151"
  - family-names: "Edwards"
    given-names: "Robert A"
    orcid: "https://orcid.org/0000-0001-8383-8949"
  - family-names: "Bouras"
    given-names: "George"
    orcid: "https://orcid.org/0000-0002-5885-4186"
  - family-names: "Kieser"
    given-names: "Silas"
    orcid: "https://orcid.org/0000-0002-5935-9734"
title: "Snaketool: a Cookiecutter profile for making a Snakemake-based bioinformatics tool."
version: 1.0.0
doi:
date-released: 2022
url: "https://github.com/beardymcjohnface/Snaketool"
preferred-citation:
  type: article
  authors:
  - family-names: "Roach"
    given-names: "Michael J"
    orcid: "https://orcid.org/0000-0003-1488-5148"
  - family-names: "Pierce-Ward"
    given-names: "N Tessa"
    orcid: "https://orcid.org/0000-0002-2942-5331"
  - family-names: "Suchecki"
    given-names: "Radoslaw"
    orcid: "https://orcid.org/0000-0003-4992-9497"
  - family-names: "Mallawaarachchi"
    given-names: "Vijini"
    orcid: "https://orcid.org/0000-0002-2651-8719"
  - family-names: "Papudeshi"
    given-names: "Bhavya"
    orcid: "https://orcid.org/0000-0001-5359-3100"
  - family-names: "Handley"
    given-names: "Scott A"
    orcid: "https://orcid.org/0000-0002-2143-6570"
  - family-names: "Brown"
    given-names: "C Titus"
    orcid: "https://orcid.org/0000-0001-6001-2677"
  - family-names: "Watson-Haigh"
    given-names: "Nathan S"
    orcid: "https://orcid.org/0000-0002-7935-6151"
  - family-names: "Edwards"
    given-names: "Robert A"
    orcid: "https://orcid.org/0000-0001-8383-8949"
  doi: "10.1371/journal.pcbi.1010705"
  journal: "PLOS Computational Biology"
  start: e1010705
  title: "Ten simple rules and a template for creating workflows-as-applications"
  issue: 12
  volume: 18
  year: 2022

GitHub Events

Total
  • Watch event: 6
Last Year
  • Watch event: 6

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 91
  • Total Committers: 4
  • Avg Commits per committer: 22.75
  • Development Distribution Score (DDS): 0.099
Top Committers
Name Email Commits
Michael Roach b****e@g****m 82
Vijini Mallawaarachchi v****i@g****m 6
gbouras13 g****s@a****u 2
Silas Kieser S****K@u****m 1
Committer Domains (Top 20 + Academic)
adelaide.edu.au: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 3
  • Total pull requests: 5
  • Average time to close issues: 5 months
  • Average time to close pull requests: 22 days
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.8
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • beardymcjohnface (1)
  • gbouras13 (1)
  • MelinaKlostermann (1)
Pull Request Authors
  • beardymcjohnface (2)
  • Vini2 (1)
  • gbouras13 (1)
  • SilasK (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
pypi.org: my-snaketool

Snakemake-powered commandline tool to do a thing.

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 4.8%
Dependent repos count: 6.3%
Average: 13.5%
Forks count: 20.8%
Stargazers count: 22.1%
Last synced: about 1 year ago

Dependencies

{{cookiecutter.project_slug}}/setup.py pypi
  • Click >=7
  • pyyaml *
  • snakemake >=6.10.0
.github/workflows/python-app.yml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/codecov.yml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
build/environment.yaml pypi
  • click >=8.1.3
  • cookiecutter >=2.1.1
  • jinja2 >=3.0.2
  • pyyaml >=6.0
  • snakemake >=7.20.0