Add support for Apptainer container engine (#3345)

Signed-off-by: tbugfinder <tbugfinder@online.ms>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -1166,6 +1166,7 @@ class Session implements ISession {
         getContainerConfig0('shifter', engines)
         getContainerConfig0('udocker', engines)
         getContainerConfig0('singularity', engines)
+        getContainerConfig0('apptainer', engines)
         getContainerConfig0('charliecloud', engines)
 
         def enabled = engines.findAll { it.enabled?.toString() == 'true' }

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -178,6 +178,9 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names = '-with-singularity', description = 'Enable process execution in a Singularity container')
     def withSingularity
 
+    @Parameter(names = '-with-apptainer', description = 'Enable process execution in a Apptainer container')
+    def withApptainer
+
     @Parameter(names = '-with-podman', description = 'Enable process execution in a Podman container')
     def withPodman
 

modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy

@@ -252,6 +252,10 @@ class Launcher {
                 normalized << '-'
             }
 
+            else if( current == '-with-apptainer' && (i==args.size() || args[i].startsWith('-'))) {
+                normalized << '-'
+            }
+
             else if( current == '-with-charliecloud' && (i==args.size() || args[i].startsWith('-'))) {
                 normalized << '-'
             }

modules/nextflow/src/main/groovy/nextflow/container/ApptainerBuilder.groovy

@@ -0,0 +1,38 @@
+/*
+ * Copyright 2020-2022, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.container
+
+import groovy.transform.CompileStatic
+
+/**
+ * Implements a builder for Apptainer containerisation
+ *
+ * see https://apptainer.org
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class ApptainerBuilder extends SingularityBuilder {
+
+    ApptainerBuilder(String name) {
+        super(name)
+    }
+
+    @Override
+    protected String getBinaryName() { 'apptainer' }
+}

modules/nextflow/src/main/groovy/nextflow/container/ApptainerCache.groovy

@@ -0,0 +1,39 @@
+/*
+ * Copyright 2020-2022, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.container
+
+import groovy.transform.CompileStatic
+
+/**
+ * Handle caching of remote Apptainer images
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class ApptainerCache extends SingularityCache {
+
+    /** only for testing */
+    protected ApptainerCache() {}
+
+    ApptainerCache(ContainerConfig config, Map<String,String> env=null) {
+        super(config, env)
+    }
+
+    @Override
+    protected String getBinaryName() { 'apptainer' }
+}

modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy

@@ -39,6 +39,8 @@ abstract class ContainerBuilder<V extends ContainerBuilder> {
             return new PodmanBuilder(containerImage)
         if( engine == 'singularity' )
             return new SingularityBuilder(containerImage)
+        if( engine == 'apptainer' )
+            return new ApptainerBuilder(containerImage)
         if( engine == 'udocker' )
             return new UdockerBuilder(containerImage)
         if( engine == 'shifter' )

modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy

@@ -77,10 +77,19 @@ class ContainerHandler {
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-            
+
             final result = requiresCaching ? createSingularityCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
         }
+        if( engine == 'apptainer' ) {
+            final normalizedImageName = normalizeApptainerImageName(imageName)
+            if( !config.isEnabled() || !normalizedImageName )
+                return normalizedImageName
+            final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
+
+            final result = requiresCaching ? createApptainerCache(this.config, normalizedImageName) : normalizedImageName
+            return Escape.path(result)
+        }
         if( engine == 'charliecloud' ) {
             // if the imagename starts with '/' it's an absolute path
             // otherwise we assume it's in a remote registry and pull it from there
@@ -97,6 +106,11 @@ class ContainerHandler {
         new SingularityCache(new ContainerConfig(config)) .getCachePathFor(imageName) .toString()
     }
 
+    @PackageScope
+    String createApptainerCache(Map config, String imageName) {
+        new ApptainerCache(new ContainerConfig(config)) .getCachePathFor(imageName) .toString()
+    }
+
     @PackageScope
     String createCharliecloudCache(Map config, String imageName) {
         new CharliecloudCache(new ContainerConfig(config)) .getCachePathFor(imageName) .toString()
@@ -222,4 +236,40 @@ class ContainerHandler {
         return "docker://${img}"
     }
 
+    /**
+     * Normalize Apptainer image name resolving the absolute path or
+     * adding `docker://` prefix when required
+     *
+     * @param imageName The container image name
+     * @return Image name in Apptainer canonical format
+     */
+     @PackageScope
+     String normalizeApptainerImageName(String img) {
+        if( !img )
+            return null
+
+        // when starts with `/` it's an absolute image file path, just return it
+        if( img.startsWith("/") )
+            return img
+
+         // when starts with `file://` it's an image file path, resolve it against the current path
+        if (img.startsWith("file://")) {
+             return baseDir.resolve(img.substring(7)).toString()
+        }
+
+        // check if matches a protocol scheme such as `docker://xxx`
+        if( img =~ IMAGE_URL_PREFIX ) {
+            return img
+        }
+
+        // if it's the path of an existing image file return it
+        def imagePath = baseDir.resolve(img)
+        if( imagePath.exists() ) {
+            return imagePath.toString()
+        }
+
+        // in all other case it's supposed to be the name of an image in the docker hub
+        // prefix it with the `docker://` pseudo protocol used by apptainer to download it
+        return "docker://${img}"
+    }
 }

modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy

@@ -16,8 +16,10 @@
  */
 
 package nextflow.container
+
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+
 /**
  * Implements a builder for Singularity containerisation
  *
@@ -35,6 +37,8 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         this.image = name
     }
 
+    protected String getBinaryName() { 'singularity' }
+
     @Override
     SingularityBuilder params(Map params) {
 
@@ -59,6 +63,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         return this
     }
 
+    @Override
     SingularityBuilder addRunOptions(String str) {
         runOptions.add(str)
         return this
@@ -71,7 +76,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
         appendEnv(result)
 
-        result << 'singularity '
+        result << getBinaryName() << ' '
 
         if( engineOptions )
             result << engineOptions.join(' ') << ' '
@@ -107,11 +112,12 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
     }
 
     protected String prefixEnv(String key) {
-        if( key.startsWith('SINGULARITY_') )
+        final PREFIX = getBinaryName().toUpperCase()
+        if( key.startsWith(PREFIX+'_') )
             return key
-        if( key.startsWith('SINGULARITYENV_') )
+        if( key.startsWith(PREFIX+'ENV_') )
             return key
-        return "SINGULARITYENV_$key"
+        return PREFIX+'ENV_'+key
     }
 
     @Override