Nextflow Snippets

Snippet is a programming term for a small region of re-usable source code, machine code, or text, and Nextflow is both a Domain-Specific Language for writing data pipelines and a pipeline orchestrator. For more information about Nextflow, check the official site and documentation. For community training material, this link is a greaaaaaat place to start! 😃

This repository contains a collection of numerous solutions I have worked on throughout the past months as a Nextflow and nf-core Developer Advocate at Seqera Labs providing community support to numerous users around the world. I haven't saved all the snippets I created, but as I have now answered over 500 questions in this period, there are indeed quite a few I have kept when I found the solution interesting enough 😆

List of snippets by category

Below, you'll find links to Markdown documents in this repository explaining the issue followed by the snippet that solves it.

Using Channel Operators

• Get first N elements from a channel
• Get last N elements from a channel
• Filter items within a list in tuples within your channels
• Filter tuples within your channel
• Flatten multiple-item tuple to 2-item tuple keeping key
• Recreate countBy operator for channels consisting of single elements or tuples
• Set operations with channels
• Filter output channel elements based on file size or file content
• Sort lexicographically paths in a list within a tuple
• Provide multiple paths from a channel as a string to a command
• Guarantee tuple structure in a channel
• Group based on two keys, sort based on another one

Misc

• Prepare assets without running the pipeline
• Organize output files according to some pattern, and organize everything else in a different path
• Capture multiple values provided with a pipeline parameter
• Query attributes of objects
• Piping with multiple processes at the same time
• Get the publishDir paths for a specific task
• Request the maximum number of available CPU cores for a process
• Pass config settings as a command line argument instead of a config file
• Multiple instances of the same file provided to the same task
• Save configuration files used in a specific run
• Compose configurations in the nextflow.config file
• Run some processes outside containers
• Run containers of specific processes without root access

Nextflow Patterns

If you're looking for more snippets, you can find plenty at Nextflow Patterns.