🚀 cccTeqy

NGS data — Processing Automation Engine
Full-stack, production-grade, HPC-enabled epigenomics automation pipeline.

cccTeqy is a fully automated, modular, and high-performance pipeline designed to process ChIP-seq, CUT&RUN, and CUT&Tag datasets at scale — from raw FASTQ to publication-ready QC metrics, peak calls, bigWigs, and consolidated MultiQC reports.

This README reflects the latest full pipeline implementation, built around the main Bash script:
📌 run.sh** — the central engine of cccTeqy**

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✨ Features

• Full Workflow Automation: FASTQ → Peaks/QC/bigWigs/MultiQC
• Supports ChIP-seq, CUT&RUN, CUT&Tag, SE & PE
• Unified YAML-based configuration (no code editing)
• Local + HPC support: SLURM & PBS
• Advanced QC suite:
  • FastQC
  • Picard duplication metrics
  • Preseq library complexity
  • deepTools fragment profiling
  • PhantomPeak cross-correlation (NSC, RSC)
  • FRiP scoring
  • MultiQC
• Peak Calling: MACS2 (narrow/broad)
• Container-ready: Docker & Singularity configurations included
• Production documentation stack: README, CHANGELOG, WIKI

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📁 Repository Structure

cccTeqy/
│
├── run.sh                         # Main pipeline script
├── config.yaml                    # Example config
├── config.container.example.yaml  # Container-optimized config
├── samples.tsv                    # Example sample sheet
│
├── Dockerfile                     # Docker build file
├── Singularity                    # Singularity definition file
├── environment.yml                # Conda environment
├── Makefile                       # Docker/Singularity build automation
│
├── README.md                      # Main documentation (this file)
├── CHANGELOG.md                   # Version history
└── wiki/                          # Exported GitHub Wiki pages

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🔧 Requirements (Native Execution)

Install system tools if not using containers:

• bwa, samtools, bedtools
• fastqc, macs2
• picard, preseq
• deepTools: bamCoverage, bamPEFragmentSize
• Rscript, phantompeakqualtools (run_spp.R)
• multiqc

Conda option

mamba env create -f environment.yml
mamba activate cccteqy

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⚙️ Quick Start (Native Mode)

1. Configure the pipeline

A minimal working config.yaml:

project_name: MyProject
outdir: outputs
run_mode: local
threads: 16
bwa_index: /path/to/hg38/bwa/index
blacklist_bed: /path/to/hg38/blacklist.bed
rscript: Rscript
phantompeak_rscript: /opt/tools/run_spp.R

2. Prepare your sample sheet

SAMPLE_ID FASTQ1 FASTQ2 ASSAY MARK CONTROL_ID LIBTYPE
S1 R1.fq.gz R2.fq.gz CUTTAG H3K27me3 None PE

3. Run pipeline

./run.sh -c config.yaml -s samples.tsv

4. Single-sample processing

./run.sh -c config.yaml -s samples.tsv --run-single S1

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🐳 Docker Execution

The repository includes a BYO-config Dockerfile.

Build

docker build -t cccteqy:latest .

Run

docker run --rm \
  -v $PWD:/work -v /data:/data -w /work \
  cccteqy:latest ./run.sh -c config.yaml -s samples.tsv

More details: dockerhub-README.md

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📦 Singularity Execution

Build

singularity build cccteqy.sif Singularity

Run

singularity exec -B $PWD:/work -B /data:/data cccteqy.sif \
  ./run.sh -c config.yaml -s samples.tsv

More details: singularityhub-README.md

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🧪 Workflow Overview

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📚 Documentation

Full documentation available in the GitHub Wiki, including:

• Installation
• Configuration guide
• Sample sheet guide
• QC module explanations
• Developer documentation
• Troubleshooting

Wiki pages also included locally under wiki/.

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🔥 Changelog

See CHANGELOG.md.

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🧱 Container-Based Configuration Example

A lightweight configuration specifically for use inside Docker/Singularity:

project_name: DemoContainerRun
outdir: /work/outputs
run_mode: local
threads: 8
bwa_index: /data/ref/hg38/bwa/hg38
blacklist_bed: /data/ref/hg38/blacklist/hg38-blacklist.v2.bed
rscript: Rscript
phantompeak_rscript: /opt/conda/bin/run_spp.R

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🤝 Contributing

We welcome:

• New QC modules
• New peak callers
• Workflow optimizations
• Container enhancements
• Documentation improvements

Contribute here:
👉 https://github.com/ebareke/cccTeqy/issues

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🪐 License

MIT License — open, reusable, extensible.

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