README.md

About nextflow

Nextflow is a DSL workflow manager (https://www.nextflow.io/).

Training material and documentation

• nextflow tutorials
• nextflow documentation

Community-developed workflows in nextflow

The nf-core projects hosts community curated nextflow pipelines.

Running the proof of concept Nextflow pipeline

1. Install nextflow by following the instructions here
2. Optionally move the nextflow directory to a directory in your path i.e. echo $PATH and then mv nextflow usr/bin
3. Navigate to the directory where you saved example.nf
4. Run the pipeline with the following command:
   • nextflow run example.nf --ref ref.fasta[.gz] --left path/to/reads_1.fastq --right path/to/reads_2.fastq --outdir path/to/resultdir
5. Or run nextflow run example.nf --help for more information

Notes and Contribution

This pipeline is a minimal example of using nextflow. We welcome contributions to the documentation and workflow, please create an issue or submit a pull request!

How to cite Nextflow

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. doi:10.1038/nbt.3820