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 set of resource label directives MUST be provided for the module as listed in the nf-core pipeline template.

The template defines two label schemes. New and updated modules SHOULD use the axis-decomposed labels; the bundled labels are retained for backwards compatibility and are scheduled for deprecation.

1.1 Axis-decomposed labels (preferred)

Three independent axes cover CPU, memory and time. A module picks at most one label per axis and combines them to describe its resource shape:

AxisLabels (low to high)
CPUprocess_cpus_singleprocess_cpus_lowprocess_cpus_mediumprocess_cpus_high
Memoryprocess_mem_lowprocess_mem_mediumprocess_mem_high
Timeprocess_time_shortprocess_time_mediumprocess_time_long

A CPU-bound but memory-light short job declares:

main.nf
process FOO {
    label 'process_cpus_high'
    label 'process_mem_low'
    label 'process_time_short'
    ...
}

A module MAY omit a label on an axis it does not need to tune. Axes without an explicit label receive the per-process defaults defined at the top of base.config.

A module MUST NOT declare more than one label on the same axis. process_cpus_low and process_cpus_high together is invalid and is rejected by the linter.

1.2 Bundled labels (legacy)

The original label set ties CPU, memory and time together. Use exactly one per module: process_single, process_low, process_medium, or process_high. Two 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).

These labels remain functional but emit a lint warning, and SHOULD be migrated to the axis-decomposed scheme. See the migration guide for the legacy-to-axis mapping table and a recipe for site-config maintainers.

1.3 Label precedence

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, axis-decomposed labels next, and the legacy modifier labels (process_long, process_low_memory, process_high_memory) last. Stacking a modifier on top of a bundled label resolves to the modifier’s value on the axis it overrides, and the bundled values on the others.

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_cpus_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}.
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