ENCODE ATAC-seq Workflow Wrapper

Authors

• Robin Meyers @robinmeyers

Purpose

Under development

This pipeline acts as a wrapper around the ENCODE ATAC-seq workflow for running multiple samples and gathering QC metrics.

Usage

Simple

Step 1: Install workflow

Install the ATAC workflow as well as the croo and qc2tsv utilities.

Clone this repositiory and change into the new directory.

Activate the conda environment. Run the snakemake pipeline on provided test data.

$ conda activate encode-atac-seq-pipeline
$ snakemake --directory .test

Examine the outputs of the workflow in the directory .test/outs/

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 3: Execute workflow

Ensure the correct conda environment is active with

$ conda activate encode-atac-seq-pipeline

Test your configuration by performing a dry-run via

$ snakemake -n

$ snakemake -j 999 -p  --cluster-config cluster.json --profile slurm

Before running in a cluster environment, edit the cluter.json config file.

Step 4: Investigate results

The main outputs are in the <sample>/outs/ directories.

After successful execution, you can create a self-contained interactive HTML report with workflow statistics.

$ snakemake --report report.html

This report can, e.g., be forwarded to your collaborators.

Updating the workflow

If you installed the workflow by cloning the github repo, you can pull latest updates to workflow with

$ git pull --rebase

This will require you to first commit any changes you made to your configuration file before pulling new updates.

Then simply rerun the snakemake command.

Testing

Tests cases are in the subfolder .test. They are automtically executed via continuous integration with Travis CI.