github.com/snakemake-workflows/chipseq ↗
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
An animated visualization of snakemake-workflows/chipseq's Git history from April 2020 to October 2020, built by 2 contributors. The codebase reached 123 lines, mostly Python. The video runs 22 seconds.
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Language
Python
Contributors
2
Lines of Code
123
From
2020-04-15
To
2020-10-21
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About snakemake-workflows/chipseq
This is a Snakemake workflow for ChIP-seq analysis, implementing a bioinformatics pipeline for chromatin immunoprecipitation sequencing experiments. The pipeline handles peak-calling, quality control, and differential analysis of ChIP-seq data. It represents a port of the nextflow pipeline from nf-co.re/chipseq into Snakemake, a workflow management system popular in computational biology.
The workflow is designed to be flexible and reproducible, allowing users to configure analysis parameters through YAML config files and sample sheets. It supports local execution across multiple cores as well as distributed computing on cluster environments using technologies like DRMAA or grid job schedulers. The pipeline integrates conda for environment management and Singularity for containerization, ensuring consistent software dependencies and reproducibility across different computing systems.
The project targets bioinformaticians and researchers performing ChIP-seq analyses. It includes testing infrastructure with continuous integration through GitHub Actions, and provides functionality to generate interactive HTML reports of analysis results. Users can easily synchronize their local copies with upstream updates and contribute improvements back to the original repository through standard GitHub workflows.
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