Resource requirements

The keywords “MUST”, “MUST NOT”, “SHOULD”, etc. are to be interpreted as described in RFC 2119.

1 Use of labels in modules

An appropriate resource label MUST be provided for the module as listed in the nf-core pipeline template.

The template (since nf-core/tools:4.1.0) defines two kinds of labels:

• Bundled labels set CPU, memory and time together. Use exactly one per module: process_single, process_low, process_medium, or process_high.
• Modifier labels override a single axis and SHOULD be stacked on top of a bundled label: process_long (extends time), process_low_memory (drops memory), process_high_memory (raises memory).

When a process matches more than one withLabel: block, Nextflow applies them in the order they appear in the config file. The order of the label directives in the process itself does not affect precedence. The nf-core template defines bundled labels first and modifier labels after, so modifier labels always overwrite the corresponding bundled value.

2 Source of multiple threads or cores value

If the tool supports multi-threading, provide the appropriate parameter using the Nextflow task variable. For example, --threads $task.cpus.

If the tool does not support multi-threading, consider process_single unless large amounts of RAM are required.

3 Specifying multiple threads for piped commands

If a module contains multiple tools that support multi-threading (e.g., piping output into a samtools command), assign CPUs per tool:

• [task.cpus] is supplied unchanged when a process uses multiple cores.
• If one tool is multi-threaded and another uses a single thread, specify directly in the command itself. For example, with ${task.cpus}.