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A modular Hi-C mapping pipeline for reproducible data analysis.

The distiller pipeline aims to provide the following functionality:

  • Align the sequences of Hi-C molecules to the reference genome
  • Parse .sam alignment and form files with Hi-C pairs
  • Filter PCR duplicates
  • Aggregate pairs into binned matrices of Hi-C interactions



  • java 8
  • nextflow
  • singularity or docker (the latter should be able to run w/o root privileges, tutorial)

To setup a new project, execute the following line in the project folder:

$ nextflow clone open2c/distiller-nf ./

This will download the distiller pipeline and the configuration files.


  • configure the location of the input files and other project details in project.yml
  • configure additional parameters in nextflow.config
  • use provided hardware configurations using local and cluster profiles, or provide your own using custom profile

Launch distiller depending on your usage scenario:

  1. default hardware settings ./configs/local.config with your project.yml:
$ nextflow run -params-file project.yml
  1. cluster hardware profile ./configs/cluster.config with your project.yml:
$ nextflow run -params-file project.yml -profile cluster
  1. custom hardware profile with your own configuration file and your project.yml:
$ nextflow run -params-file project.yml -profile custom --custom_config /full/path/to/your.config

Test example

In a new project folder, execute:

$ nextflow clone mirnylab/distiller-nf  ./
$ bash ./test/
$ nextflow -params-file ./test/test_project.yml