nf-core · pinin4fjords · May 6, 2026 · May 6, 2026 · May 6, 2026 · May 13, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,9 @@
 - accept `process_low_memory` as a standard module label ([#4264](https://github.com/nf-core/tools/pull/4264))
 - improve linting for `modules.json` to add support for only installing subworkflows from a repository and provide more explicit error messages ([#4287](https://github.com/nf-core/tools/pull/4287))
 - improve singularity_tag linting check (add skip, handle exceptions correctly, check against oras) ([#4358](https://github.com/nf-core/tools/pull/4358))
+- accept axis-decomposed `process_cpus_*` and `process_mem_*` labels alongside the legacy combined labels ([#XXXX](https://github.com/nf-core/tools/pull/XXXX))
+- accept axis-decomposed `process_cpus_*` and `process_mem_*` labels alongside the legacy combined labels ([#4265](https://github.com/nf-core/tools/pull/4265))
+- accept axis-decomposed `process_cpus_*`, `process_mem_*` and `process_time_*` labels alongside the legacy combined labels ([#4265](https://github.com/nf-core/tools/pull/4265))
 
 ### Modules
 
@@ -33,6 +36,9 @@
 - fix dead link ([#4307](https://github.com/nf-core/tools/pull/4307))
 - remove date placeholder from changelog title ([#4333](https://github.com/nf-core/tools/pull/4333))
 - Fix publishDir configuration in modules.config for multiqc ([#4347](https://github.com/nf-core/tools/pull/4347))
+- add axis-decomposed `process_cpus_{single,low,medium,high}` and `process_mem_{low,medium,high}` labels to `base.config`; legacy combined labels remain in place pending deprecation ([#XXXX](https://github.com/nf-core/tools/pull/XXXX))
+- add axis-decomposed `process_cpus_{single,low,medium,high}` and `process_mem_{low,medium,high}` labels to `base.config`; legacy combined labels remain in place pending deprecation ([#4265](https://github.com/nf-core/tools/pull/4265))
+- add axis-decomposed `process_cpus_{single,low,medium,high}`, `process_mem_{low,medium,high}` and `process_time_{short,medium,long}` labels to `base.config`; legacy combined labels remain in place pending deprecation ([#4265](https://github.com/nf-core/tools/pull/4265))
 
 #### Version updates
 

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
@@ -244,6 +244,18 @@ def _get_bioconda_tool(self):
 
     def _get_module_structure_components(self):
         process_label_defaults = [
+            # Axis-decomposed labels (preferred)
+            "process_cpus_single",
+            "process_cpus_low",
+            "process_cpus_medium",
+            "process_cpus_high",
+            "process_mem_low",
+            "process_mem_medium",
+            "process_mem_high",
+            "process_time_short",
+            "process_time_medium",
+            "process_time_long",
+            # Legacy combined labels (kept for backwards compatibility, to be deprecated)
             "process_single",
             "process_low",
             "process_medium",

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
@@ -69,7 +69,26 @@ def main_nf(
       equal the number of ``emit:`` outputs whose name starts with ``versions``.
       A warning is issued if a legacy YAML-based ``versions`` emit is used instead
       of a topic output.
-
+    * ``process_standard_label``: Process labels should follow the standard format.
+      A warning is issued if a legacy label is used. Allowed standard labels are:
+          "process_cpus_single",
+          "process_cpus_low",
+          "process_cpus_medium",
+          "process_cpus_high",
+          "process_mem_low",
+          "process_mem_medium",
+          "process_mem_high",
+          "process_time_short",
+          "process_time_medium",
+          "process_time_long"
+      Legacy labels are:
+          "process_single",
+          "process_low",
+          "process_medium",
+          "process_high",
+          "process_long",
+          "process_low_memory",
+          "process_high_memory"
     """
 
     inputs: list[str] = []
@@ -558,6 +577,19 @@ def check_process_name_format(self, process_name, component_name):
 
 def check_process_labels(self, lines):
     correct_process_labels = [
+        # Axis-decomposed labels (preferred)
+        "process_cpus_single",
+        "process_cpus_low",
+        "process_cpus_medium",
+        "process_cpus_high",
+        "process_mem_low",
+        "process_mem_medium",
+        "process_mem_high",
+        "process_time_short",
+        "process_time_medium",
+        "process_time_long",
+    ]
+    legacy_process_labels = [
         "process_single",
         "process_low",
         "process_medium",
@@ -569,11 +601,11 @@ def check_process_labels(self, lines):
     all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")]
     bad_labels = []
     good_labels = []
+    legacy_labels = []
     if len(all_labels) > 0:
         for label in all_labels:
-            try:
-                label = re.match(r"^label\s+'?\"?([a-zA-Z0-9_-]+)'?\"?$", label).group(1)
-            except AttributeError:
+            match = re.match(r"^label\s+'?\"?([a-zA-Z0-9_-]+)'?\"?$", label)
+            if match is None:
                 self.warned.append(
                     (
                         "main_nf",
@@ -583,21 +615,46 @@ def check_process_labels(self, lines):
                     )
                 )
                 continue
-            if label not in correct_process_labels:
+            label = match.group(1)
+            if label not in correct_process_labels and label not in legacy_process_labels:
                 bad_labels.append(label)
+            if label in legacy_process_labels:
+                legacy_labels.append(label)
             else:
                 good_labels.append(label)
-        if len(good_labels) > 1:
+        if legacy_labels:
+            self.warned.append(
+                (
+                    "main_nf",
+                    "process_standard_label",
+                    f"Deprecated process label found: `{legacy_labels[0]}`. Use the new standard labels instead:  https://nf-co.re/docs/developing/migration-guides/resource-labels",
+                    self.main_nf,
+                )
+            )
+        axes = [label.split("_")[1] for label in good_labels if len(label.split("_")) > 1]
+        if len(axes) != len(set(axes)):
+            conflicting = [
+                label
+                for label in good_labels
+                if axes.count(label.split("_")[1] if len(label.split("_")) > 1 else "") > 1
+            ]
             self.warned.append(
                 (
                     "main_nf",
                     "process_standard_label",
-                    f"Conflicting process labels found: `{'`,`'.join(good_labels)}`",
+                    f"Conflicting process labels found: `{'`,`'.join(conflicting)}`",
+                    self.main_nf,
+                )
+            )
+        elif good_labels:
+            self.passed.append(
+                (
+                    "main_nf",
+                    "process_standard_label",
+                    f"Correct process labels: `{'`,`'.join(good_labels)}`",
                     self.main_nf,
                 )
             )
-        elif len(good_labels) == 1:
-            self.passed.append(("main_nf", "process_standard_label", "Correct process label", self.main_nf))
         else:
             self.warned.append(("main_nf", "process_standard_label", "Standard process label not found", self.main_nf))
         if len(bad_labels) > 0:
@@ -618,6 +675,7 @@ def check_process_labels(self, lines):
                     self.main_nf,
                 )
             )
+
     else:
         self.warned.append(("main_nf", "process_standard_label", "Process label not specified", self.main_nf))
 

diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config
@@ -26,6 +26,51 @@ process {
     //        adding in your local modules too.
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+
+    //
+    // Resource labels for independently controlling the default amount
+    // of CPUs, memory, and time requests a process makes to a scheduler.
+    //
+    // TODO nf-core: adjust all CPU, memory, and time resource requests to work with 'average' data for the pipeline.
+    //        Default resource usage limits are intentionally generous and are may not be suitable.
+    //        It is highly recommended to modify these settings to suit your pipeline.
+    //
+    withLabel:process_cpus_single {
+        cpus   = { 1                    }
+    }
+    withLabel:process_cpus_low {
+        cpus   = { 2     * task.attempt }
+    }
+    withLabel:process_cpus_medium {
+        cpus   = { 6     * task.attempt }
+    }
+    withLabel:process_cpus_high {
+        cpus   = { 12    * task.attempt }
+    }
+    withLabel:process_mem_low {
+        memory = { 1.GB  * task.attempt }
+    }
+    withLabel:process_mem_medium {
+        memory = { 12.GB * task.attempt }
+    }
+    withLabel:process_mem_high {
+        memory = { 72.GB * task.attempt }
+    }
+    withLabel:process_time_short {
+        time   = { 1.h   * task.attempt }
+    }
+    withLabel:process_time_medium {
+        time   = { 8.h   * task.attempt }
+    }
+    withLabel:process_time_long {
+        time   = { 20.h  * task.attempt }
+    }
+
+    //
+    // Legacy combined labels. Kept for backwards compatibility while the
+    // ecosystem migrates to the axis-decomposed labels above; these will be
+    // deprecated in a future release.
+    //
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB * task.attempt }

diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
@@ -67,19 +67,25 @@ def test_process_name_format(process_name, component_name, passed, warned, faile
 @pytest.mark.parametrize(
     "content,passed,warned,failed",
     [
-        # Valid process label
-        ("label 'process_high'\ncpus 12", 1, 0, 0),
-        # Non-alphanumeric characters in label
+        # Valid new-style axis-decomposed label
+        ("label 'process_cpus_high'\ncpus 12", 1, 0, 0),
+        # Multiple axis-decomposed labels on different axes — allowed
+        ("label 'process_cpus_high'\nlabel 'process_mem_low'\ncpus 12", 1, 0, 0),
+        # Same axis twice — conflict
+        ("label 'process_cpus_high'\nlabel 'process_cpus_low'\ncpus 12", 0, 1, 0),
+        # Legacy label warns (no new-style label present, so also warns "not found")
+        ("label 'process_high'\ncpus 12", 0, 2, 0),
+        # Two legacy labels warn legacy + not-found (distinct, so no dup warn)
+        ("label 'process_high'\nlabel 'process_low'\ncpus 12", 0, 2, 0),
+        # Duplicate legacy labels: not-found + legacy + duplicate
+        ("label 'process_high'\nlabel 'process_high'\ncpus 12", 0, 3, 0),
+        # Non-alphanumeric characters in label: non-alphanumeric warn + not-found warn
         ("label 'a:label:with:colons'\ncpus 12", 0, 2, 0),
-        # Conflicting labels
-        ("label 'process_high'\nlabel 'process_low'\ncpus 12", 0, 1, 0),
-        # Duplicate labels
-        ("label 'process_high'\nlabel 'process_high'\ncpus 12", 0, 2, 0),
-        # Valid and non-standard labels
-        ("label 'process_high'\nlabel 'process_extra_label'\ncpus 12", 1, 1, 0),
-        # Non-standard label only
-        ("label 'process_extra_label'\ncpus 12", 0, 2, 0),
-        # Non-standard duplicates without quotes
+        # Non-standard (bad) label only: passes axis check but warns non-standard
+        ("label 'process_extra_label'\ncpus 12", 1, 1, 0),
+        # Legacy + non-standard: passes axis check, warns legacy and non-standard
+        ("label 'process_high'\nlabel 'process_extra_label'\ncpus 12", 1, 2, 0),
+        # Non-standard duplicates without quotes: conflict + non-standard + duplicate
         ("label process_extra_label\nlabel process_extra_label\ncpus 12", 0, 3, 0),
         # No label found
         ("cpus 12", 0, 1, 0),
@@ -386,7 +392,11 @@ def test_topics_and_emits_version_check(self):
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="bamstats/generalstats")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        # assert len(module_lint.warned) == 0, f"Expected 0 warnings, got {[x.__dict__ for x in module_lint.warned]}"
+        # TODO: once modules are migrated to axis-decomposed labels, remove the filter and assert len(module_lint.warned) == 0
+        non_label_warned = [w for w in module_lint.warned if w.lint_test != "process_standard_label"]
+        assert len(non_label_warned) == 0, (
+            f"Expected 0 non-label warnings, got {[x.__dict__ for x in non_label_warned]}"
+        )
 
         assert len(module_lint.passed) > 0