Nextflow Patterns

A curated collection of Nextflow implementation patterns

Basic patterns

• Channel duplication
• Sort FilePairs by sample name
• Create key to combine channels

Scatter executions

• Process per file path
• Process per file chunk
• Process per file pairs
• Process per file range
• Process per CSV record
• Process per file output

Gather results

• Process all outputs altogether
• Process outputs into groups
• Collect outputs into a file

Organize outputs

• Store process outputs
• Store outputs matching a glob pattern
• Store outputs renaming files

Other

• Get process work directory
• Ignore failing process
• State dependency

Advanced patterns

• Conditional process resources
• Conditional process executions
• Skip process execution
• Feedback loop
• Optional input
• Optional output
• Process when empty
• Task batching