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: about 2 months 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 (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-09-25T16:08:05.000Z (almost 5 years ago)
- Last Synced: 2025-02-17T23:47:47.644Z (5 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
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.
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}.