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Nextflow is a workflow manager that allows the creationof portable, scalable, reproducible pipelines.

Nextflow gives the possibility to separate the configuration and the logic of thepipeline in different files.

Nextflow has a very strong support for different execution systems, so that you cantest your pipeline locally, but then deploy it in your cluster (using the installedscheduler, such as Slurm or PBS), or to the cloud!

A simple workflow to assemble prokaryotic genomes, annotate them with Prokka, andgathering statistics to prepare a MultiQC report.

This typical workflow processes a set of multiple samples (filtering, assemblying,annotating), while for other steps will collect multiple outputs to producea summary (QUAST for assemblys statistics, MultiQC report).

Blue blocks are executed once per sample, while gray dataset are collector, and are executedonce per project.

graph TD; style input fill:#ff9,stroke:#333,stroke-width:2px classDef collapse fill:#EEE,stroke:#333,stroke-width:2px classDef multi fill:#9FF,stroke:#333,troke-width:2px input(FASTQ INPUT) --> SUBSAMPLE:::multi; SUBSAMPLE --> FASTP:::multi; FASTP --> ASSEMBLY:::multi; ASSEMBLY --> QUAST:::collapse; ASSEMBLY --> PROKKA:::multi; ASSEMBLY --> ABRICATE:::multi; ASSEMBLY --> MLST:::multi; ABRICATE --> SUMMARY:::collapse; SUMMARY --> MULTIQC:::collapse; MLST --> MULTIQC:::collapse; QUAST --> MULTIQC; PROKKA --> MULTIQC;

• Learning Nextflow in 2022, blog post by Evan Floden & Alain Coletta
• Nextflow tutorial (Carpentries)
• nf-core community, a set of high quality bioinformatics pipeline backed by a fantastic community: the pipelines, their YouTube channel and their Slack channels are all worth checking
• Video: introduction to MultiQC, MultiQC is a great tool that makes any pipeline better, and Nextflow can make great use of it