Migrating to axis-decomposed resource labels

The bundled resource labels (process_low, process_medium, process_high, process_long, process_high_memory) are being replaced by axis-decomposed labels (process_cpus_*, process_mem_*, process_time_*) that tune CPU, memory and time independently. Bundled labels still work and emit a lint warning; they are removed after a two-release deprecation window.

The full scheme is defined in Resource requirements; the rationale is in nf-core/proposals#139.

Why migrate

• Most tools scale on only one axis; bundled labels over-provision the others, often by hundreds of times.
• Common shapes like “many CPUs, little memory” or “moderate CPUs, high memory” cannot be expressed cleanly with bundled labels.
• Pipelines have been working around this with locally invented labels (process_high_cpu etc.), which diverge across the ecosystem.

Default mapping

Start from this table. The process_low row is opinionated: its 12 GB legacy default is closer to process_mem_medium than process_mem_low, so module authors should sanity-check the choice rather than apply it mechanically.

A process_high module becomes:

 process FOO {
-    label 'process_high'
+    label 'process_cpus_high'
+    label 'process_mem_high'
+    label 'process_time_long'
     ...
 }

A process_medium + process_high_memory stack becomes:

 process FOO {
-    label 'process_medium'
-    label 'process_high_memory'
+    label 'process_cpus_medium'
+    label 'process_mem_high'
+    label 'process_time_medium'
     ...
 }

Omit any axis label that matches the template default; that is the canonical way to say “this axis does not need to be tuned”.

Modules and pipelines

1. Replace each legacy label on the process with the axis labels from the table, adjusting per the tool’s real scaling profile.
2. Apply the same change to any conf/base.config overrides in the pipeline, and drop pipeline-local label definitions that just duplicate the template.
3. Run nf-core modules lint to confirm the new labels are recognised.

The bundled-label withLabel: blocks in the template’s base.config are removed by the nf-core template sync; they should not be edited by hand.

Institutional site configs

Sites that override withLabel: process_* need parallel overrides for the new axis labels. The default translation is the mapping table above; institutions with custom tiering may want different values per axis.

A sed recipe to seed the CPU axis from existing overrides (always review the diff before committing):

sed -E '
  s/withLabel: ?process_low\b/withLabel:process_cpus_low/;
  s/withLabel: ?process_medium\b/withLabel:process_cpus_medium/;
  s/withLabel: ?process_high\b/withLabel:process_cpus_high/;
' conf/site.config

The recipe rewrites the CPU axis only. Memory and time overrides do not translate one-to-one and need review by hand.

Deprecation timeline

See also

• Resource requirements
• RFC: nf-core/proposals#139
• Template change: nf-core/tools#4265