Skip to content

telatin/nextflow-example

Repository files navigation

Open in Gitpod

A simple DSL2 pipeline

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

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

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

What are we doing

A simple workflow to assemble prokaryotic genomes, annotate them with Prokka, and gathering 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 produce a summary (QUAST for assemblys statistics, MultiQC report).

Blue blocks are executed once per sample, while gray dataset are collector, and are executed once 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;
Loading

Resources