nfcore/mrimorph is a bioinformatics pipeline used for the analysis of brain morphometry MRI imaging data.
The pipeline is built using Nextflow, 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.
i. Install nextflow
ii. Install one of docker or singularity.
iii. Download the pipeline and test it on a minimal dataset with a single command
nextflow run nf-core/mrimorph -profile test,<docker/singularity/institute>Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile institutein your command. This will enable eitherdockerorsingularityand set the appropriate execution settings for your local compute environment.
iv. Start running your own analysis!
nextflow run nf-core/mrimorph -profile <docker/singularity/institute> --input '*.img'See usage docs for all of the available options when running the pipeline.
The nf-core/mrimorph pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
The pipeline was originally written by The Bioinformatics & Biostatistics Group in collaboration with Jonny Kohl, Patty Wai and Bernard Siow from The Francis Crick Institute, London and Ma Da from Simon Fraser University, British Columbia, Canada.
The pipeline was developed by Harshil Patel.
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).
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.