An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
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/.<!-- TODO nf-core: Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the major pipeline sections and the types of output it produces. You're giving an overview to someone new to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction --> <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. --> <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline --> <!-- ## Usage :::note If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. ::: <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets. Explain what rows and columns represent. For instance (please edit as appropriate): First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). --> <!-- Now, you can run the pipeline using: --> <!-- TODO nf-core: update the following command to include all required parameters for a minimal example --> <!-- ```bash nextflow run nf-core/mcmicro \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR> ``` -->
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*;
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
Citations<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --> <!-- If you use nf-core/mcmicro for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --> <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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
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.