Nextflow for Reproducible Scientific Analysis

First key point. Brief Answer to questions. (FIXME)

A workflow is a series of tasks to process data.

A workflow framework is a set of tools that allow you to compose tasks, connect them together, and process data.

There are many workflow frameworks available.

Nextflow is reproducible, portable, simple, extensible, well designed, open source, and supported.

Nextflow is written in the Groovy computer language.

Channels and Processes are the fundamental data structures of Nextflow.

A workflow script is run using nextflow run <script.nf>.

A process has five parts: directives, input, output, when, and the script.

Each process task runs from it’s own directory.

A process only executes when there is a complete process input declaration.

Selected process output can be saved to a folder using publishDir.

Directives control process execution behaviour.

Channels pass data into and out of processes.

There are two types of channel, queue and value channels.

Each channel must have it’s own input channel.

Channels can be manipulated using channel operators.

First key point. Brief Answer to questions. (FIXME)

Commands are expected to be available from the shell PATH.

Environment modules can provide centrally managed software environments.

Conda can provide user managed software environments

Container platforms can provide self-contained software environments, and are recommended for reproducibility.

The workflow block describes the workflow.

Workflows can be modularised.

Channel forking is now implicit.

Use an organised folder structure.

Start by making process templates for code.

Refactor once the workflow logic is in place.

Make a test data set.

Nextflow can run workflows from version control platforms.

Version control can aid workflow development.

First key point. Brief Answer to questions. (FIXME)

First key point. Brief Answer to questions. (FIXME)

First key point. Brief Answer to questions. (FIXME)