chipseq-smk-pipeline

ChIP-Seq processing pipeline - snakemake version of washu pipeline.
Developed with SnakeCharm plugin for PyCharm IDE.

Configuration

The only tool required to launch the pipeline is conda.

• If conda is not installed, follow the instructions at Conda website.
• Navigate to repository directory.

Create a Conda environment for snakemake:

$ conda env create --file ./environment.yaml --name snakemake

Activate the newly created environment:

$ source activate snakemake

Launch

Run the pipeline:

$ snakemake all [--cores <cores>] --use-conda --directory <work_dir> --config genome=<genome> fastq_dir=<fastq_dir>

P.S: Use --config to override default options from ./config.yaml file

QSUB

Configure profile for qsub with Torque scheduler with name generic_qsub

$ mkdir -p ~/.config/snakemake
$ cd ~/.config/snakemake
$ cookiecutter https://github.com/iromeo/generic.git

Example of ATAC-Seq processing on qsub

$ snakemake all --use-conda --profile generic_qsub --cluster-config qsub_config.yaml --jobs 150 \
    --directory <work_dir> \
    --config fastq_dir=<fastq_dir> genome=<genome> \
    macs2_params="-q 0.05 -f BAMPE --nomodel --nolambda -B --call-summits" \
    span_params="--fragment 0" bin=100 bowtie2_params="-X 2000 --dovetail"

P.S: Use --config to override default options from ./config.yaml file

Pipeline Description

Pipeline aligned FASTQ or gzipped FASTQ reads, defined in config.yaml. Reads folder is a relative path in pipeline working directory and defined by fastq_dir property. FASTQ reads extension is defined by fastq_ext property, e.g. could be fq, fq.gz, fastq, fastq.gz.

Folder	Description
./config.yaml	Default pipeline options
./trimmed	Trimmed FASTQ file, if trim_reads option is True. BAM files will contain trimmed reads in this case
./bams	BAMs with aligned reads, MAPQ >= 30
./deduplicated	Deduplicated version of ./bams files
./macs2	MACS2 peaks
./sicer	SICER peaks
./span	SPAN peaks
./multiqc	MultiQC reports for different steps
./qc	QC Reports
./logs	Shell commands logs

Useful links

• SnakeCharm plugin
• PyCharm IDE
• Snakemake workflow management system
• JetBrains Research BioLabs homepage