nextflow

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 nextflow/example.nf \
         --left $PWD/test_data/reads_1.fq.gz \
         --right $PWD/test_data/reads_2.fq.gz \
         --ref $PWD/test_data/transcriptome.fa
   

5. Enable the use Docker containers adding the following option to the above command line: -with-docker quay.io/nextflow/rnaseq-nf:v1.0

Note: input files requires the use of absolute paths

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