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

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

Launch distiller as:

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

In a new project folder, execute:

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