a modular Hi-C mapping pipeline
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README.md

distiller-nf

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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

Installation

Requirements:

  • java 7/8
  • nextflow
  • docker (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 mirnylab/distiller ./

This will download the distiller pipeline and the configuration files.

Then:

  • configure the location of the input files and other project details in project.yml
  • configure the hardware/system details in nextflow.config and/or in ./configs/*.config

Launch distiller as:

$ nextflow distiller.nf -params-file project.yml

Test example

In a new project folder, execute:

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