Introduction


Figure 1

Grid with the characteristics of: Reproducible; same data, same analysis. Replicable; different data, same analysis. Robust; same data, different analysis. And generalisable; different data, different analysis; Research
Grid with the characteristics of: Reproducible; same data, same analysis. Replicable; different data, same analysis. Robust; same data, different analysis. And generalisable; different data, different analysis; Research

Figure 2

File management system
File management system

Figure 3

Workflow manager template folder build your own workflow
Workflow manager template folder build your own workflow

Hello Nextflow


Figure 1

Diagram of a computational process within a bioinformatics workflow. The image features a large, central, rounded rectangle labeled 'process' with a smaller rectangle inside it labeled 'script', indicating the code or commands that are being implemented. Above the script box, there is a smaller inset labeled 'Executors' with three icons: a desktop computer labeled 'Local', a stack of servers labeled 'High Performance Compute Cluster', and a cloud symbol labeled 'Cloud Compute'. These represent the different computing environments where the script can be implemented. To the left of the process box is a green left-pointing arrowhead, suggesting input into the process, and to the right is a yellow right-pointing arrowhead, indicating the direction of output from the process.
Runtime


Parameters


Channels


Figure 1

Channel files

Modules


Figure 1

Process Flow
Process Flow

Modules Part 2


Workflow


Operators


Reporting


Nextflow configuration


Auxiliary Tools


Figure 1

Arrows indicate users making changes and synchronizing their work with the repository.
Arrows indicate users making changes and synchronizing their work with the repository.

Resuming a Workflow


Portability of Workflow


Figure 1

Archie West, Edinburgh Parallel Computing Centre (EPCC), Institutions University of Glasgow, University of Edinburgh, University of St. Andrews, University of Strathclyde
Archie West, Edinburgh Parallel Computing Centre (EPCC), Institutions University of Glasgow, University of Edinburgh, University of St. Andrews, University of Strathclyde

Figure 2

Nextflow workflow managers supporting multiple compute environments including local computers, high performance computing clusters with Slurm, and cloud services such as AWS and Google Cloud.
Nextflow workflow managers supporting multiple compute environments including local computers, high performance computing clusters with Slurm, and cloud services such as AWS and Google Cloud.

Figure 3

Batch job submission on compute cluster using the workflow profile slurm.
Batch job submission on compute cluster using the workflow profile slurm.