epigen/atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

Overview

Topics: snakemake atac-seq python bioinformatics workflow ngs pipeline biomedical-data-science bash

Latest release: v2.0.2, Last update: 2025-05-27

Linting: linting: failed, Formatting: formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.

When using Mamba, run

mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/epigen/atacseq_pipeline . --tag v2.0.2

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Configuration

You need one configuration file and one annotation file to run the complete workflow. You can use the provided examples as starting point. If in doubt read the comments in the config and/or try the default values.

  • project configuration (config/config.yaml): different for every project/dataset and configures the processing and quantification. The fields are described within the file.

  • annotation.csv: CSV file consisting of one technical sequencing unit per row (i.e., one sample can include multiple sequencing units, hence mutliple rows) and 4 mandatory columns:

    • sample_name (first column!)

    • read_type: “single” or “paired”.

    • bam_file: path to the raw/unaligned/unmapped uBAM file.

    • pass_qc: number between 0 (not used for downstream steps e.g., quantification) and 1. Every sample with pass_qc>0 is included in the downstream quantification and annotation steps.

    • (optional) additional sample metadata columns can be added and indicated for inclusion in the report.

Set workflow-specific resources or command line arguments (CLI) in the workflow profile workflow/profiles/default.config.yaml, which supersedes global Snakemake profiles.

Two examples (hg38 & mm10) are provided in the test/ directory and are pre-filled with resource locations from the respective Zenodo download.

Linting and formatting

Linting results

1Using workflow specific profile workflow/profiles/default for setting default command line arguments.
2FileNotFoundError in file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/Snakefile", line 28:
3[Errno 2] No such file or directory: '/path/to/MyATACproject_pipeline_annotation.csv'
4  File "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/Snakefile", line 28, in <module>
5  File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
6  File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read
7  File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
8  File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
9  File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py", line 873, in get_handle

Formatting results

 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/resources.smk":  Formatted content is different from original
 3[DEBUG] 
 4[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/common.smk":  Formatted content is different from original
 5[DEBUG] 
 6[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/report.smk":  Formatted content is different from original
 7[DEBUG] 
 8[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/export.smk":  Formatted content is different from original
 9[DEBUG] 
10[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/processing.smk":  Formatted content is different from original
11[DEBUG] 
12[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/quantification.smk":  Formatted content is different from original
13[DEBUG] 
14[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/Snakefile":  Formatted content is different from original
15[DEBUG] 
16[DEBUG] In file "/tmp/tmp1smhtn9s/epigen-atacseq_pipeline-043630e/workflow/rules/region_annotation.smk":  Formatted content is different from original
17[INFO] 8 file(s) would be changed 😬
18
19snakefmt version: 0.11.0