Make DSL2 default syntax

Author: pditommaso

docs/basic.rst

@@ -28,19 +28,18 @@ and ultimately the pipeline execution flow itself, is implicitly defined by thes
 
 A Nextflow script looks like this::
 
+    // Declare syntax version
+    nextflow.enable.dsl=2
     // Script parameters
     params.query = "/some/data/sample.fa"
     params.db = "/some/path/pdb"
 
-    db = file(params.db)
-    query_ch = Channel.fromPath(params.query)
-
     process blastSearch {
-        input:
-        file query from query_ch
-
-        output:
-        file "top_hits.txt" into top_hits_ch
+      input:
+        path query
+        path db
+      output:
+        path "top_hits.txt"
 
         """
         blastp -db $db -query $query -outfmt 6 > blast_result
@@ -49,18 +48,21 @@ A Nextflow script looks like this::
     }
 
     process extractTopHits {
-        input:
-        file top_hits from top_hits_ch
+      input:
+        path top_hits
 
-        output:
-        file "sequences.txt" into sequences_ch
+      output:
+        path "sequences.txt"
 
         """
         blastdbcmd -db $db -entry_batch $top_hits > sequences.txt
         """
     }
 
-
+    workflow {
+       def query_ch = Channel.fromPath(params.query)
+       blastSearch(query_ch, params.db) | extractTopHits | view
+    }
 
 The above example defines two processes. Their execution order is not determined by the fact that the ``blastSearch``
 process comes before ``extractTopHits`` in the script (it could also be written the other way around).

docs/config.rst

@@ -965,6 +965,7 @@ NXF_ANSI_SUMMARY                Enables/disables ANSI completion summary: `true|
 NXF_SCM_FILE                    Defines the path location of the SCM config file (requires version ``20.10.0`` or later).
 NXF_PARAMS_FILE                 Defines the path location of the pipeline parameters file (requires version ``20.10.0`` or later).
 NXF_DISABLE_JOBS_CANCELLATION   Disables the cancellation of child jobs on workflow execution termination (requires ``21.12.0-edge`` or later).
+NXF_DEFAULT_DSL                 Defines the DSL version version that should be used in not specified otherwise in the script of config file (default: ``2``, requires version ``22.03.0-edge`` or later)
 JAVA_HOME                       Defines the path location of the Java VM installation used to run Nextflow.
 JAVA_CMD                        Defines the path location of the Java binary command used to launch Nextflow.
 HTTP_PROXY                      Defines the HTTP proxy server. As of version ``21.06.0-edge``, proxy authentication is supported providing the credentials in the proxy URL e.g. ``http://user:[email protected]:port``.

docs/dsl2.rst

@@ -12,6 +12,16 @@ your workflow script::
 
     nextflow.enable.dsl=2
 
+.. tip::
+  As of version ``22.03.0-edge`` Nextflow defaults to DSL 2 if no version version is specified explicitly.
+  You can restore the previous behavior setting in into your environment the following variable::
+
+    export NXF_DEFAULT_DSL=1
+
+
+.. note::
+  As of version ``22.03.0-edge`` the DSL version specification (either 1 or 2) can also be specified in
+  the Nextflow configuration file using the same notation shown above.
 
 Function
 ========

docs/getstarted.rst

@@ -87,34 +87,33 @@ Your first script
 Copy the following example into your favourite text editor and save it to a file named ``tutorial.nf`` ::
 
     #!/usr/bin/env nextflow
+    nextflow.enable.dsl=2
 
     params.str = 'Hello world!'
 
     process splitLetters {
+      output:
+        path 'chunk_*'
 
-        output:
-        file 'chunk_*' into letters
-
-        """
+      """
         printf '${params.str}' | split -b 6 - chunk_
-        """
+      """
     }
 
-
     process convertToUpper {
+      input:
+        file x
+      output:
+        stdout
 
-        input:
-        file x from letters.flatten()
-
-        output:
-        stdout result
-
-        """
+      """
         cat $x | tr '[a-z]' '[A-Z]'
-        """
+      """
     }
 
-    result.view { it.trim() }
+    workflow {
+      splitLetters | flatten | convertToUpper | view { it.trim() }
+    }
 
 
 This script defines two processes. The first splits a string into 6-character chunks, writing each one to a file with the prefix ``chunk_``,

modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy

@@ -19,7 +19,7 @@ import static nextflow.extension.Bolts.DATETIME_FORMAT
 @EqualsAndHashCode
 class NextflowMeta {
 
-    private static final Pattern DSL2_DECLARATION = ~/(?m)^\s*(nextflow\.(preview|enable)\.dsl\s*=\s*2)\s*;?\s*$/
+    private static final Pattern DSL_DECLARATION = ~/(?m)^\s*(nextflow\.(preview|enable)\.dsl\s*=\s*(\d))\s*;?\s*$/
 
     private static boolean ignoreWarnDsl2 = System.getenv('NXF_IGNORE_WARN_DSL2')=='true'
 
@@ -28,6 +28,7 @@ class NextflowMeta {
         abstract boolean strict
     }
 
+    @Deprecated
     @Slf4j
     static class Preview implements Flags {
         volatile float dsl
@@ -62,6 +63,7 @@ class NextflowMeta {
      */
     final String timestamp
 
+    @Deprecated
     final Preview preview = new Preview()
 
     final Features enable = new Features()
@@ -107,38 +109,41 @@ class NextflowMeta {
     }
 
     boolean isDsl2() {
-        preview.dsl == 2 || enable.dsl == 2
+        enable.dsl == 2
     }
 
     boolean isDsl2Final() {
         enable.dsl == 2
     }
 
-    void enableDsl2(boolean preview=false) {
-        if( preview )
-            this.preview.dsl = 2
-        else
-            this.enable.dsl = 2
+    void enableDsl2() {
+        this.enable.dsl = 2
     }
 
     void disableDsl2() {
         enable.dsl = 1
-        preview.dsl = 1
     }
 
     boolean isStrictModeEnabled() {
-        preview.strict || enable.strict
+        return enable.strict
     }
 
     void checkDsl2Mode(String script) {
-        final matcher = DSL2_DECLARATION.matcher(script)
+        final matcher = DSL_DECLARATION.matcher(script)
         final mode = matcher.find() ? matcher.group(2) : null
         if( !mode )
             return
-        if( mode == 'enable' )
-            enableDsl2()
+        final ver = matcher.group(3)
+        if( mode == 'enable' ) {
+            if( ver=='2' )
+                enableDsl2()
+            else if( ver=='1' )
+                disableDsl2()
+            else
+                throw new IllegalArgumentException("Unknown nextflow DSL version: ${ver}")
+        }
         else if( mode == 'preview' )
-            enableDsl2(true)
+            throw new IllegalArgumentException("Preview nextflow mode 'preview' is not supported anymore -- Please use `nextflow.enable.dsl=2` instead")
         else
             throw new IllegalArgumentException("Unknown nextflow mode=${matcher.group(1)}")
     }

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

@@ -34,6 +34,7 @@ import nextflow.Const
 import nextflow.NF
 import nextflow.NextflowMeta
 import nextflow.config.ConfigBuilder
+import nextflow.config.ConfigMap
 import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
 import nextflow.plugin.Plugins
@@ -221,6 +222,9 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-entry'], description = 'Entry workflow name to be executed', arity = 1)
     String entryName
 
+    @Parameter(names=['-dsl1'], description = 'Execute the workflow using DSL1 syntax')
+    boolean dsl1
+
     @Parameter(names=['-dsl2'], description = 'Execute the workflow using DSL2 syntax')
     boolean dsl2
 
@@ -269,9 +273,9 @@ class CmdRun extends CmdBase implements HubOptions {
         if( offline && latest )
             throw new AbortOperationException("Command line options `-latest` and `-offline` cannot be specified at the same time")
 
-        if( dsl2 )
-            NextflowMeta.instance.enableDsl2()
-        
+        if( dsl1 && dsl2 )
+            throw new AbortOperationException("Command line options `-dsl1` and `-dsl2` cannot be specified at the same time")
+
         checkRunName()
 
         log.info "N E X T F L O W  ~  version ${Const.APP_VER}"
@@ -286,6 +290,9 @@ class CmdRun extends CmdBase implements HubOptions {
                 .setBaseDir(scriptFile.parent)
         final config = builder .build()
 
+        // check DSL syntax in the config
+        launchInfo(config, scriptFile)
+
         // -- load plugins
         final cfg = plugins ? [plugins: plugins.tokenize(',')] : config
         Plugins.setup( cfg )
@@ -327,6 +334,31 @@ class CmdRun extends CmdBase implements HubOptions {
         runner.execute(scriptArgs, this.entryName)
     }
 
+    protected void launchInfo(ConfigMap config, ScriptFile scriptFile) {
+        // -- try determine DSL version from config file
+        final DSL2 = '2'
+        final DSL1 = '1'
+        final defaultDsl = env.get('NXF_DEFAULT_DSL') ?: DSL2
+        final dsl = config.navigate('nextflow.enable.dsl', defaultDsl) as String
+        if( dsl=='2' )
+            NextflowMeta.instance.enableDsl2()
+        else if( dsl=='1' )
+            NextflowMeta.instance.disableDsl2()
+        else
+            throw new AbortOperationException("Invalid Nextflow DSL value: $dsl")
+
+        // -- script can still override the DSL version
+        NextflowMeta.instance.checkDsl2Mode(scriptFile.main.text)
+
+        // -- show launch info 
+        final ver = NF.dsl2 ? DSL2 : DSL1
+        if( scriptFile.repository )
+            log.info "Launching `$scriptFile.repository` [$runName] DSL${ver} - revision: ${scriptFile.revisionInfo}"
+        else
+            log.info "Launching `$scriptFile.source` [$runName] DSL${ver} - revision: ${scriptFile.getScriptId()?.substring(0,10)}"
+
+    }
+
     protected void checkRunName() {
         if( runName == 'last' )
             throw new AbortOperationException("Not a valid run name: `last`")
@@ -405,9 +437,7 @@ class CmdRun extends CmdBase implements HubOptions {
         if( script.exists() ) {
             if( revision )
                 throw new AbortOperationException("Revision option cannot be used running a script")
-            def result = new ScriptFile(script)
-            log.info "Launching `$script` [$runName] - revision: ${result.getScriptId()?.substring(0,10)}"
-            return result
+            return new ScriptFile(script)
         }
 
         /*
@@ -431,7 +461,6 @@ class CmdRun extends CmdBase implements HubOptions {
             manager.checkout(revision)
             manager.updateModules()
             final scriptFile = manager.getScriptFile(mainScript)
-            log.info "Launching `$repo` [$runName] - revision: ${scriptFile.revisionInfo}"
             if( checkForUpdate && !offline )
                 manager.checkRemoteStatus(scriptFile.revisionInfo)
             // return the script file

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -665,6 +665,16 @@ class ConfigBuilder {
             config.tower.endpoint = cmdRun.withTower
         }
 
+        // -- nextflow setting
+        if( cmdRun.dsl1 || cmdRun.dsl2 ) {
+            if( config.nextflow !instanceof Map )
+                config.nextflow = [:]
+            if( cmdRun.dsl1 )
+                config.nextflow.enable.dsl = 1
+            if( cmdRun.dsl2 )
+                config.nextflow.enable.dsl = 2
+        }
+
         // -- add the command line parameters to the 'taskConfig' object
         if( cmdRun.hasParams() )
             config.params = mergeMaps( (Map)config.params, cmdRun.parsedParams(configVars()), NF.strictMode )

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

@@ -33,6 +33,11 @@ import nextflow.util.CacheHelper
 @ToString(includeNames = true)
 class ScriptFile {
 
+    /**
+     * Pipeline source file as specified by the user (it may be a relative path
+     */
+    Path source
+
     /**
      * Pipeline main script file
      */
@@ -86,6 +91,7 @@ class ScriptFile {
 
     ScriptFile( Path file ) {
         assert file
+        source = file
         main = file.complete()
         localPath = main.parent
     }

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

@@ -168,7 +168,6 @@ class ScriptParser {
     ScriptParser parse(String scriptText, GroovyShell interpreter) {
         final String clazzName = computeClassName(scriptText)
         try {
-            NextflowMeta.instance.checkDsl2Mode(scriptText)
             script = (BaseScript)interpreter.parse(scriptText, clazzName)
             final meta = ScriptMeta.get(script)
             meta.setScriptPath(scriptPath)

modules/nextflow/src/test/groovy/nextflow/NextflowMetaTest.groovy

@@ -50,16 +50,13 @@ class NextflowMetaTest extends Specification {
         where:
         DSL2    | FINAL | SCRIPT
         false   | false | 'hello'
-        false   | false | 'nextflow.preview.dsl=1'
-        and:
-        true    | false | 'nextflow.preview.dsl=2'
-        true    | false | 'nextflow.preview.dsl = 2'
-        true    | false | 'nextflow.preview.dsl =  2;'
-        true    | false | '#!/bin/env nextflow\nnextflow.preview.dsl=2\nprintln foo'
+        false   | false | 'nextflow.enable.dsl=1'
         and:
         true    | true | 'nextflow.enable.dsl=2'
         true    | true | 'nextflow.enable.dsl = 2'
         true    | true | 'nextflow.enable.dsl =  2;'
         true    | true | '#!/bin/env nextflow\nnextflow.enable.dsl=2\nprintln foo'
+        and:
+        false   | false | 'nextflow.enable.dsl = 1'
     }
 }