https://github.com/drpatelh/nf-core-mrimorph
UNDER CONSTRUCTION: Mouse brain morphometry analysis pipeline for MRI imaging data
https://github.com/drpatelh/nf-core-mrimorph
morphometry mri mri-brain mri-images nextflow nf-core pipeline workflow
Last synced: 2 months ago
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UNDER CONSTRUCTION: Mouse brain morphometry analysis pipeline for MRI imaging data
- Host: GitHub
- URL: https://github.com/drpatelh/nf-core-mrimorph
- Owner: drpatelh
- License: mit
- Created: 2019-10-07T16:51:23.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2019-12-17T10:54:56.000Z (over 5 years ago)
- Last Synced: 2025-01-13T12:46:36.843Z (4 months ago)
- Topics: morphometry, mri, mri-brain, mri-images, nextflow, nf-core, pipeline, workflow
- Language: Nextflow
- Homepage: http://nf-co.re
- Size: 127 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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## Introduction
**nfcore/mrimorph** is a bioinformatics pipeline used for the analysis of brain morphometry MRI imaging data.
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
## Quick Start
i. Install [`nextflow`](https://nf-co.re/usage/installation)
ii. Install one of [`docker`](https://docs.docker.com/engine/installation/) or [`singularity`](https://www.sylabs.io/guides/3.0/user-guide/).
iii. Download the pipeline and test it on a minimal dataset with a single command
```bash
nextflow run nf-core/mrimorph -profile test,
```
> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile institute` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
iv. Start running your own analysis!
```bash
nextflow run nf-core/mrimorph -profile --input '*.img'
```
See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
## Documentation
The nf-core/mrimorph pipeline comes with documentation about the pipeline, found in the `docs/` directory:
1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
## Credits
The pipeline was originally written by [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) in collaboration with [Jonny Kohl](https://www.crick.ac.uk/research/labs/johannes-kohl), [Patty Wai](mailto:[email protected]) and [Bernard Siow](https://www.crick.ac.uk/research/find-a-researcher/bernard-siow) from [The Francis Crick Institute](https://www.crick.ac.uk/), London and [Ma Da](mailto:[email protected]) from [Simon Fraser University](https://www.sfu.ca/), British Columbia, Canada.
The pipeline was developed by [Harshil Patel](mailto:[email protected]).
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/nf-core/mrimorph) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citation
You can cite the `nf-core` pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).