This repository is obsolete and not maintained anymore. You can check out the new and extended ATAC-seq pipeline from here.

ATAC-seq Data Processing Pipeline

This pipeline is developed for processing raw/unaligned ATAC-seq data to generate peak calls, a QC report and motif discovery results. The pipeline can process both single-end and paired-end reads in unaligned BAM format.

1 - Installation

1. Clone this repository.
2. Install the software listed in the required_software.txt.
3. Install atacseq plugin for MultiQC: python3 /path/to/atacseq_pipeline/multiqc_atacseq/setup.py install
4. Collect all the reference data listed in the atacseq_config.yaml file and update the file with correct paths. This file contains the pipeline configurations common among different projects.

2 - Running the pipeline

2.1 - Setting up a new analysis/project

For each project you need to prepare a project config (.yaml) file and a sample annotations sheet (.csv). You can set the project name, output path, genome version etc. in the project config file. Sample annotations sheet should contain one line for each input raw BAM file, multiple files with the same sample_name will be merged during the alignment step. Make sure that the data_source template of each file is configured in the config file under the data_sources: attribute. These templates will be used to generate the full path of the input files.

2.2 - Running the analysis

1. Generate the input files for the cromwell WDL engine:

python3 /path/to/atacseq_pipeline/configurator.py \
    -p /path/to/atacseq_pipeline/atacseq_config.yaml \
    -c /path/to/my_project_config.yaml

2. Go to the project output path and run cromwell workflow manager:

cd /my/project/path
java -Dconfig.file=/path/to/atacseq_pipeline/backends/slurm.conf -Xmx2g \
    -jar /path/to/cromwell-52.jar run /path/to/atacseq_pipeline/atacseq.wdl \
    --inputs config_files/BSA_0000_test_atac.inputs.json

2.3 Creating the QC report

After the pipeline has finished, you can run MultiQC to generate a QC report:

multiqc -c /path/to/my_project_config.yaml /my/project/path