hustal/rnasequmi repository overview

This pipeline analysis rnaseq with UMI.

⁠Introduction

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.

⁠Quick Start

i. Install nextflow⁠

ii. Install one of docker⁠, singularity⁠ or conda⁠

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run nf-core/rnasequmi -profile test,<docker/singularity/conda>

iv. Start running your own analysis!

nextflow run nf-core/rnasequmi -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37

See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The nf-core/rnasequmi pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation⁠
2. Pipeline configuration
   • Local installation⁠
   • Adding your own system config⁠
   • Reference genomes⁠
3. Running the pipeline⁠
4. Output and how to interpret the results⁠
5. Troubleshooting⁠

⁠Credits

nf-core/rnasequmi was originally written by Husain Talukdar.

⁠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 Slack⁠ (you can join with this invite⁠).

⁠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.