open2c/distiller-nf

A modular Hi-C mapping pipeline

distiller-nf

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 8
• nextflow version 22.10.x or earlier
• 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.

Then:

• 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 distiller.nf -params-file project.yml

2. cluster hardware profile ./configs/cluster.config with your project.yml:

$ nextflow run distiller.nf -params-file project.yml -profile cluster

3. custom hardware profile with your own configuration file and your project.yml:

$ nextflow run distiller.nf -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/setup_test.sh
$ nextflow distiller.nf -params-file ./test/test_project.yml 

Nextflow and DSL version note

Distiller was originally designed for DSL1 syntax of nextflow. Nextflow stopped supporting DSL1 with 23.X.X update.

We recommend fixing the nextflow version:

conda install -c bioconda "nextflow==22.10"

Distiller has been recently re-implemented in DSL2: https://github.com/open2c/distiller-nf/tree/distiller_dsl2.

DSL2 version is still the beta version under testing.