DiffMethSeq

A NextFlow pipeline to perform differential methylation analysis from bismark-aligned files

NOTE: UNDER DEVELOPMENT

• Description
• Workflow
• Running Environment
  • Conda
  • Docker
  • Singularity/Apptainer
• Input files and paths
• How to run
• Results
  

Description

Workflow

Running environment

Please update the selected environment in the nextflow.config file.

Using Conda

Conda can be used to run the pipeline. [update with yaml file- working]

Using Docker

Build the docker image using the Dockerfile. Default in nextflow.config will use jd21/r-nf:240129.

cd env docker build -t <USERNAME>/<tags> .

Using Singularity/Apptainer

Docker image can be directly used in the Singularity/Apptainer (no need to build an apptainer image for now). User can use the same docker image jd21/r-nf:240129 pull using the apptainer by changing the nextflow.config.

Input files and paths

1. formatted_designfile (required): (.tsv) with columns, 'Sample_ID', 'input_R1', 'input_R2', 'ip_R1', 'ip_R2', 'Group_ID' \
2. compare_string (required): 'treatedvscontrol' (or whatever group you have to compare)\
3. cov_dir (required for edgeR analysis): Path to the directory of bismark-generated zipped coverage files (deduplicated and sorted, if required). \
4. bam_dir (required for MethylKit analysis): Path to the directory of bismark-generated bam files. \
5. phenoGroup (required for MethylKit analysis): to know the group information, e.g. if you have 6 samples, like 'control', 'patient', 'control', 'patient', 'control', 'patient', then the file needs a line like this - c(0,1,0,1,0,1,0,1).

NOTE: It is possible to run either EdgeR or MethylKit.

How to run

1. Load Nextflow module: ml nextflow-23.10.1
2. docker installation required
3. Load Singularity module: ml singularity-3.8.3

```

differential methylation analysis

nextflow run main.nf -profile docker \ --formatteddesignfile ./data/Samplesheet.csv \ --comparestr ./data/comparefile.txt \ --covdir data/ \ --bamdir /bismark/deduplicated/sortedbam/ \ --phenoGroup ./data/treatment.txt ```

Results

The pipeline will generates three directories - edgeR - MethylKit - pipeline_info

Credits

• Main Author:

  • Jyotirmoy Das (@JD2112)

• Collaborators:

Citation

Das, J. (2025). DiffMethSeq (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14762150

HELP/FAQ/Troubleshooting

Please create issues on github.

Acknowledgement

We would like to acknowledge the Core Facility, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden and Clinical Genomics Linköping, Science for Life Laboratory, Sweden for their support.