Skip to content

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

License

Notifications You must be signed in to change notification settings

RobJY/mcmicro-nf-core

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

nf-core/mcmicro

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Get help on SlackFollow on TwitterFollow on MastodonWatch on YouTube

Introduction

Warning

We are currently in the process of porting the original MCMICRO to nf-core. This pipeline is therefore in active development.

nf-core/mcmicro is a nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.

If you want to run the original MCMICRO pipeline outside of nf-core, please see https://mcmicro.org/.

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Contributions and Support

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 the Slack #mcmicro channel (you can join with this invite).

Citations

If you use nf-core/mcmicro for your analysis, please cite it using the following article: Schapiro et al. 2022 Nat. Methods

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

About

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

Resources

License

Code of conduct

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • Nextflow 95.3%
  • Groovy 2.5%
  • HTML 2.2%