CLI v2

docs/cli.md

@@ -1282,14 +1282,11 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 : Disable process execution with Docker.
 
 `-without-podman`
-: Disable process execution in a Podman container.
+: Disable process execution with Podman.
 
 `-without-spack`
 : Disable process execution with Spack.
 
-`-without-wave`
-: Disable the use of Wave containers.
-
 `-w, -work-dir` (`work`)
 : Directory where intermediate result files are stored.
 
@@ -1512,3 +1509,21 @@ When a command line parameter includes one or more glob characters, i.e. wildcar
 nextflow run <my script> --files "*.fasta"
 ```
 :::
+
+(cli-v2)=
+
+## CLI v2
+
+:::{versionadded} 23.10.0
+:::
+
+Nextflow now has an alternative command-line interface called `nf`, which more closely follows conventions for CLI options. In particular, long options for `nf` have two dashes, i.e. `-resume` is now `--resume`.
+
+Pipeline parameters can be specified alongside CLI options as before, as long as they are named differently. If for some reason you have a conflicting param, you can use a double dash `--` to separate it from the CLI options.
+
+The `nf` command is a near drop-in replacement, by simply using double dashes for long options. The following minor changes were also introduced:
+
+- The `plugins` command was removed (use `plugin` instead)
+- The `secrets put` command was removed (use `secrets set` instead)
+- The `-deep` option was renamed to `--depth` for `clone`, `pull`, and `run`
+- The `-without-*` options were removed from the `run` command

launch-v1.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+#
+#  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.
+
+cwd="$(realpath "$(dirname "$0")")"
+
+MAIN_CLASS="nextflow.cli.Launcher" "${cwd}/launch.sh" "$@"

launch-v2.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+#
+#  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.
+
+cwd="$(realpath "$(dirname "$0")")"
+
+MAIN_CLASS="nextflow.cli.v2.Launcher" "${cwd}/launch.sh" "$@"

modules/nextflow/build.gradle

@@ -44,6 +44,7 @@ dependencies {
     api 'jline:jline:2.9'
     api 'org.pf4j:pf4j:3.10.0'
     api 'dev.failsafe:failsafe:3.1.0'
+    api 'info.picocli:picocli-groovy:4.7.1'
 
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
 

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

@@ -432,10 +432,7 @@ class Session implements ISession {
     }
 
     /**
-     * Given the `run` command line options creates the required {@link TraceObserver}s
-     *
-     * @param runOpts The {@code CmdRun} object holding the run command options
-     * @return A list of {@link TraceObserver} objects or an empty list
+     * Creates the required {@link TraceObserver}s for the workflow run.
      */
     @PackageScope
     List<TraceObserver> createObservers() {

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

@@ -28,79 +28,100 @@ import org.fusesource.jansi.Ansi
  * @author Paolo Di Tommaso <[email protected]>
  */
 @Slf4j
-class CliOptions {
+abstract class CliOptions {
+
+    abstract Boolean getAnsiLogCli()
+    abstract boolean isBackground()
+    abstract List<String> getConfig()
+    abstract List<String> getDebug()
+    abstract boolean getIgnoreConfigIncludes()
+    abstract String getLogFile()
+    abstract boolean isQuiet()
+    abstract boolean getRemoteDebug()
+    abstract String getSyslog()
+    abstract List<String> getTrace()
+    abstract List<String> getUserConfig()
+    abstract boolean getVersion()
+    abstract void setAnsiLog(boolean value)
+    abstract void setBackground(boolean value)
+
+    static class V1 extends CliOptions {
+
+        /**
+         * The packages to debug
+         */
+        @Parameter(hidden = true, names='-debug')
+        List<String> debug
+
+        @Parameter(names=['-log'], description = 'Set nextflow log file path')
+        String logFile
+
+        @Parameter(names=['-c','-config'], description = 'Add the specified file to configuration set')
+        List<String> userConfig
+
+        @Parameter(names=['-config-ignore-includes'], description = 'Disable the parsing of config includes')
+        boolean ignoreConfigIncludes
+
+        @Parameter(names=['-C'], description = 'Use the specified configuration file(s) overriding any defaults')
+        List<String> config
+
+        /**
+         * the packages to trace
+         */
+        @Parameter(names='-trace', description = 'Enable trace level logging for the specified package name - multiple packages can be provided separating them with a comma e.g. \'-trace nextflow,io.seqera\'')
+        List<String> trace
+
+        /**
+         * Enable syslog appender
+         */
+        @Parameter(names = ['-syslog'], description = 'Send logs to syslog server (eg. localhost:514)' )
+        String syslog
+
+        /**
+         * Print out the version number and exit
+         */
+        @Parameter(names = ['-v','-version'], description = 'Print the program version')
+        boolean version
+
+        /**
+         * Print out the 'help' and exit
+         */
+        @Parameter(names = ['-h'], description = 'Print this help', help = true)
+        boolean help
+
+        @Parameter(names = ['-q','-quiet'], description = 'Do not print information messages' )
+        boolean quiet
+
+        @Parameter(names = ['-bg'], description = 'Execute nextflow in background', arity = 0)
+        boolean background
+
+        @DynamicParameter(names = ['-D'], description = 'Set JVM properties' )
+        Map<String,String> jvmOpts = [:]
+
+        @Parameter(names = ['-self-update'], description = 'Update nextflow to the latest version', arity = 0, hidden = true)
+        boolean selfUpdate
+
+        @Parameter(names=['-remote-debug'], description = "Enable JVM interactive remote debugging (experimental)")
+        boolean remoteDebug
+
+        Boolean ansiLogCli
+
+        void setAnsiLog(boolean value) { ansiLogCli = value }
 
-    /**
-     * The packages to debug
-     */
-    @Parameter(hidden = true, names='-debug')
-    List<String> debug
-
-    @Parameter(names=['-log'], description = 'Set nextflow log file path')
-    String logFile
-
-    @Parameter(names=['-c','-config'], description = 'Add the specified file to configuration set')
-    List<String> userConfig
-
-    @Parameter(names=['-config-ignore-includes'], description = 'Disable the parsing of config includes')
-    boolean ignoreConfigIncludes
-
-    @Parameter(names=['-C'], description = 'Use the specified configuration file(s) overriding any defaults')
-    List<String> config
-
-    /**
-     * the packages to trace
-     */
-    @Parameter(names='-trace', description = 'Enable trace level logging for the specified package name - multiple packages can be provided separating them with a comma e.g. \'-trace nextflow,io.seqera\'')
-    List<String> trace
-
-    /**
-     * Enable syslog appender
-     */
-    @Parameter(names = ['-syslog'], description = 'Send logs to syslog server (eg. localhost:514)' )
-    String syslog
-
-    /**
-     * Print out the version number and exit
-     */
-    @Parameter(names = ['-v','-version'], description = 'Print the program version')
-    boolean version
-
-    /**
-     * Print out the 'help' and exit
-     */
-    @Parameter(names = ['-h'], description = 'Print this help', help = true)
-    boolean help
-
-    @Parameter(names = ['-q','-quiet'], description = 'Do not print information messages' )
-    boolean quiet
-
-    @Parameter(names = ['-bg'], description = 'Execute nextflow in background', arity = 0)
-    boolean background
-
-    @DynamicParameter(names = ['-D'], description = 'Set JVM properties' )
-    Map<String,String> jvmOpts = [:]
-
-    @Parameter(names = ['-self-update'], description = 'Update nextflow to the latest version', arity = 0, hidden = true)
-    boolean selfUpdate
-
-    @Parameter(names=['-remote-debug'], description = "Enable JVM interactive remote debugging (experimental)")
-    boolean remoteDebug
-
-    Boolean ansiLog
+    }
 
     boolean getAnsiLog() {
-        if( ansiLog && quiet )
+        if( ansiLogCli && quiet )
             throw new AbortOperationException("Command line options `quiet` and `ansi-log` cannot be used together")
 
-        if( ansiLog != null )
-            return ansiLog
+        if( ansiLogCli != null )
+            return ansiLogCli
 
         if( background )
-            return ansiLog = false
+            return ansiLogCli = false
 
         if( quiet )
-            return ansiLog = false
+            return ansiLogCli = false
 
         final env = System.getenv('NXF_ANSI_LOG')
         if( env ) try {
@@ -113,7 +134,7 @@ class CliOptions {
     }
 
     boolean hasAnsiLogFlag() {
-        ansiLog==true || System.getenv('NXF_ANSI_LOG')=='true'
+        ansiLogCli==true || System.getenv('NXF_ANSI_LOG')=='true'
     }
 
 }

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

@@ -17,12 +17,14 @@
 package nextflow.cli
 
 import com.beust.jcommander.Parameter
+import groovy.transform.CompileStatic
 
 /**
  * Implement command shared methods
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
+@CompileStatic
 abstract class CmdBase implements Runnable {
 
     private Launcher launcher