{"id":24186560,"url":"https://github.com/drpatelh/nf-core-mrimorph","last_synced_at":"2026-02-16T08:09:16.554Z","repository":{"id":119783330,"uuid":"213437516","full_name":"drpatelh/nf-core-mrimorph","owner":"drpatelh","description":"UNDER CONSTRUCTION: Mouse brain morphometry analysis pipeline for MRI imaging data","archived":false,"fork":false,"pushed_at":"2019-12-17T10:54:56.000Z","size":130,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-10-18T21:12:05.843Z","etag":null,"topics":["morphometry","mri","mri-brain","mri-images","nextflow","nf-core","pipeline","workflow"],"latest_commit_sha":null,"homepage":"http://nf-co.re","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/drpatelh.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-10-07T16:51:23.000Z","updated_at":"2019-12-17T10:54:58.000Z","dependencies_parsed_at":null,"dependency_job_id":"625c5b48-6a1e-4a7e-bbad-907c2c064e9d","html_url":"https://github.com/drpatelh/nf-core-mrimorph","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/drpatelh/nf-core-mrimorph","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-mrimorph","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-mrimorph/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-mrimorph/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-mrimorph/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/drpatelh","download_url":"https://codeload.github.com/drpatelh/nf-core-mrimorph/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-mrimorph/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29503262,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-16T08:07:58.651Z","status":"ssl_error","status_checked_at":"2026-02-16T08:07:56.823Z","response_time":115,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["morphometry","mri","mri-brain","mri-images","nextflow","nf-core","pipeline","workflow"],"created_at":"2025-01-13T12:36:04.826Z","updated_at":"2026-02-16T08:09:16.519Z","avatar_url":"https://github.com/drpatelh.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ![nf-core/mrimorph](docs/images/nf-core-mrimorph_logo.png)\n\n[![Build Status](https://travis-ci.com/nf-core/mrimorph.svg?branch=master)](https://travis-ci.com/nf-core/mrimorph)\n[![GitHub Actions CI Status](https://github.com/nf-core/mrimorph/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mrimorph/actions)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mrimorph/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mrimorph/actions)\n[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)\n\n[![Docker](https://img.shields.io/docker/automated/nfcore/mrimorph.svg)](https://hub.docker.com/r/nfcore/mrimorph)\n\n## Introduction\n\n**nfcore/mrimorph** is a bioinformatics pipeline used for the analysis of brain morphometry MRI imaging data.\n\nThe 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.\n\n\u003c!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works --\u003e\n\n## Quick Start\n\ni. Install [`nextflow`](https://nf-co.re/usage/installation)\n\nii. Install one of [`docker`](https://docs.docker.com/engine/installation/) or [`singularity`](https://www.sylabs.io/guides/3.0/user-guide/).\n\niii. Download the pipeline and test it on a minimal dataset with a single command\n\n```bash\nnextflow run nf-core/mrimorph -profile test,\u003cdocker/singularity/institute\u003e\n```\n\n\u003e 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.\n\niv. Start running your own analysis!\n\n\u003c!-- TODO nf-core: Update the default command above used to run the pipeline --\u003e\n```bash\nnextflow run nf-core/mrimorph -profile \u003cdocker/singularity/institute\u003e --input '*.img'\n```\n\nSee [usage docs](docs/usage.md) for all of the available options when running the pipeline.\n\n## Documentation\n\nThe nf-core/mrimorph pipeline comes with documentation about the pipeline, found in the `docs/` directory:\n\n1. [Installation](https://nf-co.re/usage/installation)\n2. Pipeline configuration\n    * [Local installation](https://nf-co.re/usage/local_installation)\n    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)\n3. [Running the pipeline](docs/usage.md)\n4. [Output and how to interpret the results](docs/output.md)\n5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)\n\n## Credits\n\nThe pipeline was originally written by [The Bioinformatics \u0026 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:patty.wai@crick.ac.uk) 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:da_ma@sfu.ca) from [Simon Fraser University](https://www.sfu.ca/), British Columbia, Canada.\n\nThe pipeline was developed by [Harshil Patel](mailto:harshil.patel@crick.ac.uk).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor 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)).\n\n## Citation\n\n\u003c!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. --\u003e\n\u003c!-- If you use  nf-core/mrimorph for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --\u003e\n\nYou can cite the `nf-core` pre-print as follows:  \nEwels 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).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrpatelh%2Fnf-core-mrimorph","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdrpatelh%2Fnf-core-mrimorph","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrpatelh%2Fnf-core-mrimorph/lists"}