# distiller-nf

**Repository Path**: jiang-lichun/distiller-nf

## Basic Information

- **Project Name**: distiller-nf
- **Description**: A modular Hi-C mapping pipeline
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-11-30
- **Last Updated**: 2021-11-30

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# 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 8
- [nextflow](https://www.nextflow.io/)
- singularity or docker (the latter should be able to run w/o root privileges, 
[tutorial](https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-16-04))

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

```sh
$ 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`:
```sh
$ nextflow run distiller.nf -params-file project.yml
```
2. `cluster` hardware profile `./configs/cluster.config` with your `project.yml`:
```sh
$ nextflow run distiller.nf -params-file project.yml -profile cluster
```
3. `custom` hardware profile with your own configuration file and your `project.yml`:
```sh
$ 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:

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