https://github.com/cmdoret/vapormap

Cloud based pipeline for parallelized iterative alignment of Hi-C data
https://github.com/cmdoret/vapormap

aws-batch genomics hi-c nextflow

Last synced: 22 days ago
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Cloud based pipeline for parallelized iterative alignment of Hi-C data

• Host: GitHub
• URL: https://github.com/cmdoret/vapormap
• Owner: cmdoret
• Created: 2019-12-04T19:54:02.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2020-09-25T16:08:05.000Z (over 4 years ago)
• Last Synced: 2024-11-07T01:39:54.925Z (2 months ago)
• Topics: aws-batch, genomics, hi-c, nextflow
• Language: Nextflow
• Homepage:
• Size: 74.4 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# ![Vapormap logo](docs/vapormap_logo.svg) Vapormap

Vapormap is a cloud-based alignment pipeline for Hi-C. Each fastq file is split into a number of chunks which are all aligned in parallel on aws batch. Jobs are managed using nextflow. The pipeline has 4 profiles:

* standard: Run the pipeline on the local machine directly.

* docker: Run the pipeline on the local machine inside a docker container (requires docker).

* singularity: Run the pipeline on the local machine inside a singularity container (requires singularity).

* aws: Runs the pipeline on aws batch.

* pasteur: Profile specific to institut Pasteur's HPC, to run the pipeline via singularity in a SLURM.

![Vapormap flowchart](docs/vapormap_flowchart.svg)

Hi-C reads can be aligned using iterative mapping. All configuration is done through `nextflow.config`. When using the aws profile, you need to set the input path on a s3 bucket (e.g. "s3://dir/input/").

### Prerequisites

sdk should be installed and configured for your account. A bucket with input files should also be online.

### Installation

You can get nextflow with the following command:

```bash

wget -qO- https://get.nextflow.io | bash

```

### Usage

First, edit the parameters and paths in `nextflow.config`. Then run the pipeline using:

```bash

./nextflow run main.nf -profile docker

```

Where the profile can be any of {docker,singularity,aws,pasteur}.