Add/process.dockerfile

docs/process.md

@@ -2369,6 +2369,26 @@ This directive is only used by certain executors. Refer to the {ref}`executor-pa
 
 See also: [cpus](#cpus), [memory](#memory), [queue](#queue) and [Dynamic computing resources](#dynamic-computing-resources).
 
+(process-waveDockerfile)=
+
+### waveDockerfile
+
+The `waveDockerfile` directive allows you to execute the process script in a [Docker](http://docker.io) container, through the specification of the file path for the corresponding Dockerfile recipe.
+
+This directive can only be used in conjunction with the {ref}`wave-page` service, which requires a Docker daemon to be running in machine where the pipeline is executed.
+
+For example:
+
+```groovy
+process runThisInWaveContainer {
+  waveDockerfile 'Dockerfile'
+
+  """
+  <your holy Dockerfile recipe here>
+  """
+}
+```
+
 ### Dynamic directives
 
 A directive can be assigned *dynamically*, during the process execution, so that its actual value can be evaluated based on the process inputs.

docs/wave.md

@@ -60,13 +60,15 @@ tower {
 
 Wave can build and provision container images on-demand for your Nextflow pipelines.
 
-To enable this feature, add the Dockerfile of the container to be built in the {ref}`module directory <dsl2-module-directory>` where the pipeline process is defined. When Wave is enabled, it automatically uses the Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
+To enable this feature, add the Dockerfile of the container to be built in the {ref}`module directory <dsl2-module-directory>` where the pipeline process is defined. In alternative, if you want to specify a custom file path for your Dockerfile, you can do so by means of the process {ref}`process-waveDockefile` directive.
+
+When Wave is enabled, it automatically uses the provided Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
 
 :::{tip}
 Make sure the process does not declare a `container` directive, otherwise it will take precedence over the Dockerfile definition.
 :::
 
-If a process uses a `container` directive and you still want to build the container using the Dockerfile provided in the module directory, add the following setting to the pipeline config file:
+If a process uses a `container` directive and you still want to build the container using the provided Dockerfile, add the following setting to the pipeline config file:
 
 ```groovy
 wave.strategy = ['dockerfile','container']

modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy

@@ -49,6 +49,8 @@ class TaskBean implements Serializable, Cloneable {
 
     Path spackEnv
 
+    Path dockerfile
+
     List<String> moduleNames
 
     Path workDir
@@ -126,6 +128,7 @@ class TaskBean implements Serializable, Cloneable {
 
         this.condaEnv = task.getCondaEnv()
         this.spackEnv = task.getSpackEnv()
+        this.dockerfile = task.getDockerfile()
         this.moduleNames = task.config.getModule()
         this.shell = task.config.getShell() ?: BashWrapperBuilder.BASH
         this.script = task.getScript()

modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy

@@ -377,6 +377,14 @@ class TaskConfig extends LazyMap implements Cloneable {
         return get('container')
     }
 
+    Path getDockerfile() {
+        path = get('waveDockerfile')
+        if( !path )
+            return null
+
+        return (path as Path)
+    }
+
     Architecture getArchitecture() {
         final value = get('arch')
         if( value instanceof CharSequence )

modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy

@@ -611,6 +611,10 @@ class TaskRun implements Cloneable {
         cache.getCachePathFor(config.spack as String, arch)
     }
 
+    Path getDockerfile() {
+        return config.getDockerfile()
+    }
+
     protected ContainerInfo containerInfo() {
         cache0.computeIfAbsent('containerInfo', (it)-> containerInfo0())
     }

modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy

@@ -79,6 +79,7 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'storeDir',
             'tag',
             'time',
+            'waveDockerfile',
             // input-output qualifiers
             'file',
             'set',

plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy

@@ -342,9 +342,10 @@ class WaveClient {
         attrs.container = containerImage
         attrs.conda = task.config.conda as String
         attrs.spack = task.config.spack as String
-        if( bundle!=null && bundle.dockerfile ) {
+        if( task.config.getDockerfile() != null )
+            attrs.dockerfile = task.config.getDockerfile().text
+        else if( bundle!=null && bundle.dockerfile )
             attrs.dockerfile = bundle.dockerfile.text
-        }
 
         // validate request attributes
         if( config().strategy() )

plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy

@@ -209,6 +209,26 @@ class WaveClientTest extends Specification {
         !req.containerConfig.layers
     }
 
+    def 'should create request object with dockerfile in process specific location' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        and:
+        def DOCKERFILE = folder.resolve('Dockerfile'); DOCKERFILE.text = 'from foo:latest'
+        and:
+        def session = Mock(Session) { getConfig() >> [:]}
+        def wave = new WaveClient(session)
+
+        when:
+        def req = wave.makeRequest(new WaveAssets(null, null, null, null, DOCKERFILE.text, null, null))
+        then:
+        !req.containerImage
+        new String(req.containerFile.decodeBase64()) == DOCKERFILE.text
+        !req.containerConfig.layers
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
     def 'should create request object with build and cache repos' () {
         given:
         def session = Mock(Session) { getConfig() >> [wave:[build:[repository:'some/repo',cacheRepository:'some/cache']]]}
@@ -775,6 +795,35 @@ CMD [ "/bin/bash" ]
         folder?.deleteDir()
     }
 
+    def 'should create asset with dockerfile in process specific location' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def dockerfile = folder.resolve('Dockerfile'); dockerfile.text = 'from foo:latest'
+        and:
+        def session = Mock(Session) { getConfig() >> [:]}
+        def task = Mock(TaskRun) {getConfig() >> [waveDockerfile:dockerfile.toString()] }
+        and:
+        def client = new WaveClient(session)
+
+        when:
+        def assets = client.resolveAssets(task, null)
+        then:
+        assets.dockerFileContent == '''\
+                from foo:latest'''.stripIndent()
+        and:
+        assets.dockerFileContent == dockerfile.text
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.spackFile
+        !assets.condaFile
+        !assets.projectResources
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
     def 'should create asset with conda recipe' () {
         given:
         def session = Mock(Session) { getConfig() >> [:]}