distiller-nf

KO | EN

gitlite — search

#ai #typescript #go #golang #rust #deep-learning #linux #docker #macos #java #nodejs #windows #openai #open-source

(★ 105)

A modular Hi-C mapping pipeline

distiller-nf 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# distiller-nf

[![Build Status](https://travis-ci.org/open2c/distiller-nf.svg?branch=master)](https://travis-ci.org/open2c/distiller-nf)
[![Join the chat at https://gitter.im/mirnylab/distiller](https://badges.gitter.im/mirnylab/distiller.svg)](https://gitter.im/mirnylab/distiller?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[![DOI](https://zenodo.org/badge/89316568.svg)](https://zenodo.org/badge/latestdoi/89316568)

## 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

distiller-nf 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

distiller-nf

distiller-nf 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README