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distiller-nf

★ 105 Open GitHub ↗

A modular Hi-C mapping pipeline

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# 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/) version 22.10.x or earlier
- 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 
```

### Nextflow and DSL version note

Distiller was originally designed for DSL1 syntax of nextflow. 
Nextflow [stopped supporting DSL1 with 23.X.X update](https://github.com/nextflow-io/nextflow/issues/3915).

We recommend fixing the nextflow version:

```sh
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.

distiller-nf

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