add nextflow d30e48d

nextflow/plugins/nf-cloudcache/src/main/nextflow/CloudCachePlugin.groovy

@@ -0,0 +1,36 @@
+/*
+ * Copyright 2013-2026, 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
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.plugin.BasePlugin
+import org.pf4j.PluginWrapper
+/**
+ * Nextflow cloud cache plugin
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class CloudCachePlugin extends BasePlugin {
+
+    CloudCachePlugin(PluginWrapper wrapper) {
+        super(wrapper)
+    }
+
+}

nextflow/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheConfig.groovy

@@ -0,0 +1,57 @@
+/*
+ * Copyright 2013-2026, 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.cache
+
+import groovy.transform.CompileStatic
+import nextflow.config.spec.ConfigOption
+import nextflow.config.spec.ConfigScope
+import nextflow.config.spec.ScopeName
+import nextflow.script.dsl.Description
+
+/**
+ * Model cloud cache configuration
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@ScopeName("cloudcache")
+@Description("""
+    The `cloudcache` scope controls the use of object storage as cache storage for workflow execution metadata.
+""")
+@CompileStatic
+class CloudCacheConfig implements ConfigScope {
+
+    @ConfigOption
+    @Description("""
+        Enable the use of cloud cache (default: `false`).
+    """)
+    final boolean enabled
+
+    @ConfigOption
+    @Description("""
+        The path to the cloud storage bucket for cache metadata (e.g. `s3://bucket/cache`).
+    """)
+    final String path
+
+    /* required by extension point -- do not remove */
+    CloudCacheConfig() {}
+
+    CloudCacheConfig(Map opts) {
+        this.enabled = opts.enabled as boolean
+        this.path = opts.path as String
+    }
+
+}

nextflow/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy

@@ -0,0 +1,48 @@
+/*
+ * Copyright 2013-2026, 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.cache
+
+import java.nio.file.Path
+
+import groovy.transform.CompileStatic
+import nextflow.Global
+import nextflow.Session
+import nextflow.exception.AbortOperationException
+import nextflow.plugin.Priority
+/**
+ * Implements the cloud cache factory
+ *
+ * @see CloudCacheStore
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@CompileStatic
+@Priority(-10)
+class CloudCacheFactory extends CacheFactory {
+
+    @Override
+    protected CacheDB newInstance(UUID uniqueId, String runName, Path home) {
+        if( !uniqueId ) throw new AbortOperationException("Missing cache `uuid`")
+        if( !runName ) throw new AbortOperationException("Missing cache `runName`")
+        final path = (Global.session as Session).cloudCachePath
+        if( !path )
+            throw new IllegalArgumentException("Cloud-cache path not defined - use either -with-cloudcache run option or NXF_CLOUDCACHE_PATH environment variable")
+        final store = new CloudCacheStore(uniqueId, runName, path)
+        return new CacheDB(store)
+    }
+
+}

nextflow/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy

@@ -0,0 +1,160 @@
+/*
+ * Copyright 2013-2026, 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.cache
+
+import java.nio.file.Files
+import java.nio.file.NoSuchFileException
+import java.nio.file.Path
+
+import com.google.common.hash.HashCode
+import groovy.transform.CompileStatic
+import nextflow.exception.AbortOperationException
+import nextflow.extension.FilesEx
+import nextflow.util.CacheHelper
+/**
+ * Implements the cloud cache store
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@CompileStatic
+class CloudCacheStore implements CacheStore {
+
+    private final int KEY_SIZE
+
+    /** The session UUID */
+    private UUID uniqueId
+
+    /** The unique run name associated with this cache instance */
+    private String runName
+
+    /** The base path for the entire cache */
+    private Path basePath
+
+    /** The base path for this cache instance */
+    private Path dataPath
+
+    /** The path to the index file */
+    private Path indexPath
+
+    /** Index file input stream */
+    private InputStream indexReader
+
+    /** Index file output stream */
+    private OutputStream indexWriter
+
+    CloudCacheStore(UUID uniqueId, String runName, Path basePath) {
+        assert uniqueId, "Missing cloudcache 'uniqueId' argument"
+        assert runName, "Missing cloudcache 'runName' argument"
+        assert basePath, "Missing cloudcache 'basePath' argument"
+        this.KEY_SIZE = CacheHelper.hasher('x').hash().asBytes().size()
+        this.uniqueId = uniqueId
+        this.runName = runName
+        this.basePath = basePath
+        this.dataPath = this.basePath.resolve("$uniqueId")
+        this.indexPath = dataPath.resolve("index.$runName")
+    }
+
+    @Override
+    CloudCacheStore open() {
+        indexWriter = new BufferedOutputStream(Files.newOutputStream(indexPath))
+        return this
+    }
+
+    @Override
+    CloudCacheStore openForRead() {
+        if( !dataPath.exists() )
+            throw new AbortOperationException("Missing cache directory: $dataPath")
+        indexReader = Files.newInputStream(indexPath)
+        return this
+    }
+
+    @Override
+    void drop() {
+        dataPath.deleteDir()
+    }
+
+    @Override
+    void close() {
+        FilesEx.closeQuietly(indexWriter)
+    }
+
+    @Override
+    void writeIndex(HashCode key, boolean cached) {
+        indexWriter.write(key.asBytes())
+        indexWriter.write(cached ? 1 : 0)
+    }
+
+    @Override
+    void deleteIndex() {
+        indexPath.delete()
+    }
+
+    @Override
+    Iterator<Index> iterateIndex() {
+        return new Iterator<Index>() {
+            private Index next
+
+            {
+                next = fetch()
+            }
+
+            @Override
+            boolean hasNext() {
+                return next != null
+            }
+
+            @Override
+            Index next() {
+                final result = next
+                next = fetch()
+                return result
+            }
+
+            private Index fetch() {
+                byte[] key = new byte[KEY_SIZE]
+                if( indexReader.read(key) == -1 )
+                    return null
+                final cached = indexReader.read() == 1
+                return new Index(HashCode.fromBytes(key), cached)
+            }
+        }
+    }
+
+    @Override
+    byte[] getEntry(HashCode key) {
+        try {
+            return getCachePath(key).bytes
+        }
+        catch( NoSuchFileException e ) {
+            return null
+        }
+    }
+
+    @Override
+    void putEntry(HashCode key, byte[] value) {
+        getCachePath(key).bytes = value
+    }
+
+    @Override
+    void deleteEntry(HashCode key) {
+        getCachePath(key).delete()
+    }
+
+    private Path getCachePath(HashCode key) {
+        dataPath.resolve(key.toString())
+    }
+}

nextflow/plugins/nf-cloudcache/src/test/nextflow/cache/CloudCacheConfigTest.groovy

@@ -0,0 +1,43 @@
+/*
+ * Copyright 2013-2026, 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.cache
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class CloudCacheConfigTest extends Specification {
+
+    def 'should create empty config' () {
+        when:
+        def config = new CloudCacheConfig([:])
+        then:
+        !config.enabled
+        config.path == null
+    }
+
+    def 'should create config with all options' () {
+        when:
+        def config = new CloudCacheConfig([enabled: true, path: 's3://bucket/cache'])
+        then:
+        config.enabled
+        config.path == 's3://bucket/cache'
+    }
+
+}