nextflow-io · bentsherman · Jul 16, 2026
@@ -139,6 +139,12 @@ The amount of time the Apptainer pull can last, exceeding which the process is t
 
 The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
 
+##### `apptainer.resourceLimits`
+
+<AddedInVersion version="26.10" />
+
+Apply the task `cpus` and `memory` directives as container resource limits using the `--cpus` and `--memory` flags (default: `false`).
+
 ##### `apptainer.runOptions`
 
 Specify extra command line options supported by `apptainer exec`.
@@ -1974,6 +1980,12 @@ The amount of time the Singularity pull can last, after which the process is ter
 
 The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
 
+##### `singularity.resourceLimits`
+
+<AddedInVersion version="26.10" />
+
+Apply the task `cpus` and `memory` directives as container resource limits using the `--cpus` and `--memory` flags (default: `false`).
+
 ##### `singularity.runOptions`
 
 Specify extra command line options supported by `singularity exec`.

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ApptainerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ApptainerBuilder.groovy
@@ -48,6 +48,8 @@ class ApptainerBuilder extends SingularityBuilder {
         if( config.engineOptions )
             this.addEngineOptions(config.engineOptions)
 
+        this.resourceLimits = config.resourceLimits
+
         if( config.runOptions )
             this.addRunOptions(config.runOptions)
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ApptainerConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ApptainerConfig.groovy
@@ -89,6 +89,12 @@ class ApptainerConfig implements ConfigScope, ContainerConfig {
     """)
     final String registry
 
+    @ConfigOption
+    @Description("""
+        Apply the task `cpus` and `memory` directives as container resource limits using the `--cpus` and `--memory` flags (default: `false`).
+    """)
+    final boolean resourceLimits
+
     @ConfigOption
     @Description("""
         Specify extra command line options supported by `apptainer exec`.
@@ -109,6 +115,7 @@ class ApptainerConfig implements ConfigScope, ContainerConfig {
         ociAutoPull = opts.ociAutoPull as boolean
         pullTimeout = opts.pullTimeout as Duration ?: Duration.of('20min')
         registry = opts.registry
+        resourceLimits = opts.resourceLimits as boolean
         runOptions = opts.runOptions
     }
 

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -41,6 +41,8 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
     private Boolean ociMode
 
+    protected boolean resourceLimits
+
     SingularityBuilder(String name) {
         this.image = name
         this.homeMount = defaultHomeMount()
@@ -84,6 +86,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
             this.addEngineOptions(config.engineOptions)
 
         this.ociMode = config.ociMode
+        this.resourceLimits = config.resourceLimits
 
         if( config.runOptions )
             this.addRunOptions(config.runOptions)
@@ -132,6 +135,13 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( ociMode != null )
             result << (ociMode ? '--oci ' : '--no-oci ')
 
+        if( resourceLimits ) {
+            if( cpus )
+                result << "--cpus ${cpus} "
+            if( memory )
+                result << "--memory ${memory} "
+        }
+
         if( autoMounts ) {
             makeVolumes(mounts, result)
         }

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityConfig.groovy
@@ -95,6 +95,12 @@ class SingularityConfig implements ConfigScope, ContainerConfig {
     """)
     final String registry
 
+    @ConfigOption
+    @Description("""
+        Apply the task `cpus` and `memory` directives as container resource limits using the `--cpus` and `--memory` flags (default: `false`).
+    """)
+    final boolean resourceLimits
+
     @ConfigOption
     @Description("""
         Specify extra command line options supported by `singularity exec`.
@@ -116,6 +122,7 @@ class SingularityConfig implements ConfigScope, ContainerConfig {
         ociMode = opts.ociMode as Boolean
         pullTimeout = opts.pullTimeout as Duration ?: Duration.of('20min')
         registry = opts.registry
+        resourceLimits = opts.resourceLimits as boolean
         runOptions = opts.runOptions
     }
 

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
@@ -19,6 +19,7 @@ package nextflow.container
 import java.nio.file.Paths
 
 import nextflow.SysEnv
+import nextflow.util.MemoryUnit
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -220,6 +221,21 @@ class ApptainerBuilderTest extends Specification {
         cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd \\"$NXF_TASK_WORKDIR\\"; bwa --this --that file.fastq"'
     }
 
+    def 'should emit resource limits when enabled' () {
+        expect:
+        new ApptainerBuilder('busybox')
+                .setCpus(2)
+                .setMemory(new MemoryUnit('100M'))
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
+
+        new ApptainerBuilder('busybox', new ApptainerConfig(resourceLimits: true))
+                .setCpus(2)
+                .setMemory(new MemoryUnit('100M'))
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid --cpus 2 --memory 100m -B "$NXF_TASK_WORKDIR" busybox'
+    }
+
     @Unroll
     def 'test apptainer env'() {
 

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerConfigTest.groovy
@@ -33,6 +33,7 @@ class ApptainerConfigTest extends Specification {
         expect:
         config.envWhitelist == []
         config.pullTimeout.toMillis() == 20 * 60 * 1000 //20 min
+        config.resourceLimits == false
     }
 
     def 'should create config with full map'(){
@@ -48,6 +49,7 @@ class ApptainerConfigTest extends Specification {
             ociAutoPull: false,
             pullTimeout: '50s',
             registry: 'http://registry.com',
+            resourceLimits: true,
             runOptions: '--contain --writable'
         ]
         def config = new ApptainerConfig(configMap)
@@ -61,9 +63,10 @@ class ApptainerConfigTest extends Specification {
         config.libraryDir == 'libraryDir'
         config.noHttps == false
         config.ociAutoPull == false
+        config.pullTimeout.toMillis() == 50_000 // 50s
         config.registry == 'http://registry.com'
+        config.resourceLimits == true
         config.runOptions == '--contain --writable'
-        config.pullTimeout.toMillis() == 50_000 // 50s
 
     }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
@@ -19,6 +19,7 @@ package nextflow.container
 import java.nio.file.Paths
 
 import nextflow.SysEnv
+import nextflow.util.MemoryUnit
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -221,6 +222,25 @@ class SingularityBuilderTest extends Specification {
         cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd \\"$NXF_TASK_WORKDIR\\"; bwa --this --that file.fastq"'
     }
 
+    def 'should emit resource limits when enabled' () {
+        expect:
+        new SingularityBuilder('busybox')
+                .setCpus(2)
+                .setMemory(new MemoryUnit('100M'))
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
+
+        new SingularityBuilder('busybox', new SingularityConfig(resourceLimits: true))
+                .setCpus(2)
+                .setMemory(new MemoryUnit('100M'))
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid --cpus 2 --memory 100m -B "$NXF_TASK_WORKDIR" busybox'
+
+        new SingularityBuilder('busybox', new SingularityConfig(resourceLimits: true))
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
+    }
+
     @Unroll
     def 'test singularity env'() {
 

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityConfigTest.groovy
@@ -33,6 +33,7 @@ class SingularityConfigTest extends Specification {
         expect:
         config.envWhitelist == []
         config.pullTimeout.toMillis() == 20 * 60 * 1000 //20 min
+        config.resourceLimits == false
     }
 
     def 'should create config with full map'(){
@@ -48,6 +49,7 @@ class SingularityConfigTest extends Specification {
             ociAutoPull: false,
             pullTimeout: '50s',
             registry: 'http://registry.com',
+            resourceLimits: true,
             runOptions: '--contain --writable'
         ]
         def config = new SingularityConfig(configMap)
@@ -62,6 +64,7 @@ class SingularityConfigTest extends Specification {
         config.noHttps == false
         config.ociAutoPull == false
         config.registry == 'http://registry.com'
+        config.resourceLimits == true
         config.runOptions == '--contain --writable'
         config.pullTimeout.toMillis() == 50_000 // 50s