List process container images in preview mode

docs/cli.md

@@ -1070,7 +1070,12 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-preview`
 : :::{versionadded} 22.06.0-edge
   :::
-: Run the workflow script skipping the execution of all processes
+: Run the workflow script skipping the execution of all processes.
+
+`-preview-containers` (`json`)
+: :::{versionadded} 23.08.0-edge
+  :::
+: Print a preview of the containers used for each process to stdout (implicitly enables `-preview`). An optional argument specifies the output format, can be `config` or `json`.
 
 `-process.<key>=<value>`
 : Set process config options.
@@ -1106,7 +1111,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-conda`
 : Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
 
-`-with-dag` (`dag.dot`)
+`-with-dag` (`dag-<timestamp>.dot`)
 : Create pipeline DAG file.
 
 `-with-docker`
@@ -1118,7 +1123,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-podman`
 : Enable process execution in a Podman container.
 
-`-with-report` (`report.html`)
+`-with-report` (`report-<timestamp>.html`)
 : Create workflow execution HTML report.
 
 `-with-singularity`
@@ -1127,19 +1132,19 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-spack`
 : Use the specified Spack environment package or file (must end with `.yaml`)
 
-`-with-timeline` (`timeline.html`)
+`-with-timeline` (`timeline-<timestamp>.html`)
 : Create workflow execution timeline.
 
-`-with-tower`
+`-with-tower` (`https://api.tower.nf`)
 : Monitor workflow execution with [Tower](https://cloud.tower.nf/).
 
-`-with-trace` (`trace.txt`)
+`-with-trace` (`trace-<timestamp>.txt`)
 : Create workflow execution trace file.
 
-`-with-wave`
+`-with-wave` (`https://wave.seqera.io`)
 : Enable the use of Wave containers.
 
-`-with-weblog`
+`-with-weblog` (`http://localhost`)
 : Send workflow status messages via HTTP to target URL.
 
 `-without-conda`

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

@@ -178,6 +178,11 @@ class Session implements ISession {
      */
     boolean disableRemoteBinDir
 
+    /**
+     * Suppress all output from pipeline script
+     */
+    boolean quiet
+
     /**
      * Local path where script generated classes are saved
      */

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

@@ -18,6 +18,7 @@ package nextflow.cli
 
 import com.beust.jcommander.DynamicParameter
 import com.beust.jcommander.Parameter
+import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
 import org.fusesource.jansi.Ansi
@@ -30,6 +31,8 @@ import org.fusesource.jansi.Ansi
 @Slf4j
 class CliOptions {
 
+    static @PackageScope boolean quiteDefault = false
+
     /**
      * The packages to debug
      */
@@ -73,7 +76,7 @@ class CliOptions {
     boolean help
 
     @Parameter(names = ['-q','-quiet'], description = 'Do not print information messages' )
-    boolean quiet
+    boolean quiet = quiteDefault
 
     @Parameter(names = ['-bg'], description = 'Execute nextflow in background', arity = 0)
     boolean background

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

@@ -0,0 +1,88 @@
+/*
+ * Copyright 2013-2023, 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.cli
+
+import com.beust.jcommander.Parameter
+import groovy.transform.CompileStatic
+import nextflow.Session
+import nextflow.container.inspect.ContainersInspector
+
+/**
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@CompileStatic
+class CmdInspect extends CmdBase {
+
+    @Override
+    String getName() {
+        return 'inspect'
+    }
+
+    @Parameter(names=['-profile'], description = 'Choose a configuration profile')
+    String profile
+
+    @Parameter(names=['-format'], description = "Inspect output format. Either 'json' or 'config'")
+    String format = 'json'
+
+    @Parameter(names=['-c','-config'], hidden = true )
+    List<String> runConfig
+
+    @Parameter(names=['-i'], description = 'Ignore error while inspecting the pipeline configuration' )
+    boolean ignoreErrors
+
+    @Parameter(names=['-w'], description = 'Await resources to be accessible' )
+    boolean awaitMode = false
+
+    @Parameter(description = 'Project name or repository url')
+    List<String> args
+
+    {
+        // enable quite by default
+        CliOptions.quiteDefault = true
+    }
+
+    @Override
+    void run() {
+        final target = new CmdRun()
+        target.launcher = this.launcher
+        target.args = args
+        target.profile = this.profile
+        target.runConfig = this.runConfig
+        target.preview = true
+        target.previewAction = this.&applyInspect
+        target.ansiLog = false
+        // run it
+        target.run()
+    }
+
+    protected void applyInspect(Session session) {
+        // disable wave await mode when running
+        if( session.config.wave instanceof Map )
+            configAwaitMode(session.config.wave as Map)
+        // run the inspector
+        new ContainersInspector(session.dag)
+                .withFormat(format)
+                .withIgnoreErrors(ignoreErrors)
+                .printContainers()
+    }
+
+    protected void configAwaitMode(Map waveConfig) {
+        waveConfig.awaitMode = awaitMode
+    }
+}

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

@@ -273,6 +273,8 @@ class CmdRun extends CmdBase implements HubOptions {
                 : sysEnv.get('NXF_DISABLE_JOBS_CANCELLATION') as boolean
     }
 
+    Closure<Void> previewAction
+
     @Override
     String getName() { NAME }
 
@@ -343,7 +345,7 @@ class CmdRun extends CmdBase implements HubOptions {
         // -- create a new runner instance
         final runner = new ScriptRunner(config)
         runner.setScript(scriptFile)
-        runner.setPreview(this.preview)
+        runner.setPreview(this.preview, previewAction)
         runner.session.profile = profile
         runner.session.commandLine = launcher.cliString
         runner.session.ansiLog = launcher.options.ansiLog

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

@@ -102,7 +102,8 @@ class Launcher {
                 new CmdHelp(),
                 new CmdSelfUpdate(),
                 new CmdPlugins(),
-                new CmdPlugin()
+                new CmdPlugin(),
+                new CmdInspect()
         ]
 
         if(SecretsLoader.isEnabled())

modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy

@@ -0,0 +1,114 @@
+/*
+ * Copyright 2013-2023, 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.inspect
+
+import groovy.json.JsonBuilder
+import groovy.json.JsonOutput
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.dag.DAG
+import org.codehaus.groovy.util.ListHashMap
+/**
+ * Preview the list of containers used by a pipeline.
+ *
+ * @author Ben Sherman <[email protected]>
+ */
+@Slf4j
+@CompileStatic
+class ContainersInspector {
+
+    private DAG dag
+
+    private String format
+
+    private boolean ignoreErrors
+
+    ContainersInspector(DAG dag) {
+        this.dag = dag
+    }
+
+    ContainersInspector withFormat(String format) {
+        if( format !in ['config', 'json'] )
+            throw new IllegalArgumentException("Invalid format for container preview: '${format}' -- should be 'config' or 'json'")
+        this.format = format
+        return this
+    }
+
+    ContainersInspector withIgnoreErrors(boolean ignore) {
+        if( format !in ['config', 'json'] )
+            throw new IllegalArgumentException("Invalid format for container preview: '${format}' -- should be 'config' or 'json'")
+        this.ignoreErrors = ignore
+        return this
+    }
+
+    String computeContainers() {
+        log.debug "Rendering container preview"
+        final containers = getContainers()
+        if( format == 'config' )
+            return renderConfig(containers)
+        if( format == 'json' )
+            return renderJson(containers)
+        else
+            throw new IllegalStateException("Unknown containers preview format: $format")
+    }
+
+    void printContainers() {
+        final result = computeContainers()
+        if( result )
+            print result
+    }
+
+    protected Map<String,String> getContainers() {
+        final containers = new ListHashMap<String,String>()
+
+        for( def vertex : dag.vertices ) {
+            // skip nodes that are not processes
+            final process = vertex.process
+            if( !process )
+                continue
+
+            try {
+                // get container preview
+                containers[process.name] = process.inspectableTaskRun().getContainer()
+            }
+            catch (Exception e) {
+                if( ignoreErrors )
+                    log.warn "Unable to inspect container for task `$process.name` - cause: ${e.message}"
+                else
+                    throw e
+            }
+        }
+
+        return containers
+    }
+
+    protected String renderConfig(Map<String,String> containers) {
+        final result = new StringBuilder()
+        for( Map.Entry<String,String> entry : containers ) {
+            result.append("process { withName: '${entry.key}' { container = '${entry.value}' } }\n")
+        }
+
+        return result.toString()
+    }
+
+    protected String renderJson(Map<String,String> containers) {
+        final list = containers.collect( (k, v) -> [name: k, container: v] )
+        return JsonOutput.prettyPrint(new JsonBuilder(list).toString())
+    }
+
+}

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

@@ -367,6 +367,23 @@ class TaskProcessor {
 
     boolean hasErrors() { errorCount>0 }
 
+    /**
+     * Get a preview task config.
+     */
+    TaskRun inspectableTaskRun() {
+        final task = new TaskRun(
+                processor: this,
+                type: scriptType,
+                config: config.createTaskConfig(),
+                context: new TaskContext(this)
+        )
+        task.config.context = task.context
+        task.config.process = task.processor.name
+        task.config.executor = task.processor.executor.name
+
+        return task
+    }
+
     protected void checkWarn(String msg, Map opts=null) {
         if( NF.isStrictMode() )
             throw new ProcessUnrecoverableException(msg)