Add process programmatic configuration

docs/config.md

@@ -1071,6 +1071,19 @@ manifest {
 
 Read the {ref}`sharing-page` page to learn how to publish your pipeline to GitHub, BitBucket or GitLab.
 
+(config-nextflow)=
+
+### Scope `nextflow`
+
+The `nextflow` scope allows you to define some miscellaneous settings.
+
+The following settings are available:
+
+`nextflow.defaults.publishDir`
+: :::{versionadded} 23.10.0
+  :::
+: Default params for the {ref}`process-publishdir` directive. Every instance of this directive will use these defaults unless it overrides them for itself.
+
 (config-notification)=
 
 ### Scope `notification`

docs/dsl2.md

@@ -183,6 +183,28 @@ workflow {
 Optional params for a process input/output are always prefixed with a comma, except for `stdout`. Because `stdout` does not have an associated name or value like other types, the first param should not be prefixed.
 :::
 
+(dsl2-process-config)=
+
+### Process config
+
+:::{versionadded} 23.10.0
+:::
+
+A process can be configured with additional directives from a workflow by using the `config` attribute on a process. For example:
+
+```groovy
+include { foo ; foo as bar } from './module.nf'
+
+workflow {
+    foo()
+
+    bar.config.publishDir 'results', mode: 'copy'
+    bar()
+}
+```
+
+Process directives can be defined using the same syntax as in a process definition, and they are applied separately to different module aliases. In the above example, the `publishDir` directive is applied to process `bar` but not to process `foo`.
+
 ## Workflow
 
 ### Workflow definition

docs/process.md

@@ -1229,6 +1229,12 @@ By default, directives are evaluated when the process is defined. However, if th
 
 Some directives are generally available to all processes, while others depend on the `executor` currently defined.
 
+Process directives can also be defined in the Nextflow configuration using the {ref}`process <config-process>` scope.
+
+:::{versionadded} 23.10.0
+Process directives can also be defined for a particular process from the enclosing workflow. See {ref}`dsl2-process-config` for details.
+:::
+
 (process-accelerator)=
 
 ### accelerator

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

@@ -21,6 +21,8 @@ import java.util.regex.Pattern
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.Const
+import nextflow.Global
+import nextflow.Session
 import nextflow.NF
 import nextflow.ast.NextflowDSLImpl
 import nextflow.exception.ConfigParseException
@@ -842,7 +844,9 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             configProperties.put('publishDir', dirs)
         }
 
-        dirs.add(params)
+        final session = Global.session as Session
+        final defaults = session.config.navigate('nextflow.defaults.publishDir', [:]) as Map
+        dirs.add(defaults + params)
         return this
     }
 

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

@@ -88,6 +88,8 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         this.simpleName = name
         this.processName = name
         this.baseName = name
+
+        this.processConfig = new ProcessConfig(owner,processName)
     }
 
     static String stripScope(String str) {
@@ -96,11 +98,6 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
 
     protected void initialize() {
         log.trace "Process config > $processName"
-        assert processConfig==null
-
-        // the config object
-        processConfig = new ProcessConfig(owner,processName)
-
         // Invoke the code block which will return the script closure to the executed.
         // As side effect will set all the property declarations in the 'taskConfig' object.
         processConfig.throwExceptionOnMissingProperty(true)
@@ -121,6 +118,7 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         def result = (ProcessDef)super.clone()
         result.@taskBody = taskBody?.clone()
         result.@rawBody = (Closure)rawBody?.clone()
+        result.@processConfig = processConfig?.clone()
         return result
     }
 
@@ -145,7 +143,7 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
 
     String getBaseName() { baseName }
 
-    ProcessConfig getProcessConfig() { processConfig }
+    ProcessConfig getConfig() { processConfig }
 
     ChannelOut getOut() {
         if( output==null )

modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy

@@ -98,15 +98,15 @@ class ProcessDefTest extends Specification {
         def copy = proc.clone()
         copy.initialize()
         then:
-        def cfg1 = copy.processConfig.createTaskConfig()
+        def cfg1 = copy.config.createTaskConfig()
         cfg1.getCpus()==2           // taken from the generic config
         cfg1.getMemory().giga == 3  // taken from the `foo` config
 
         when:
         copy = proc.cloneWithName('flow1:bar')
         copy.initialize()
         then:
-        def cfg2 = copy.processConfig.createTaskConfig()
+        def cfg2 = copy.config.createTaskConfig()
         cfg2.getCpus()==4           // taken from the `bar` config
         cfg2.getMemory().giga == 4  // taken from the `bar` config
 
@@ -115,7 +115,7 @@ class ProcessDefTest extends Specification {
         copy = proc.cloneWithName('flow1:flow2:flow3:bar')
         copy.initialize()
         then:
-        def cfg3 = copy.processConfig.createTaskConfig()
+        def cfg3 = copy.config.createTaskConfig()
         cfg3.getCpus()==4           // <-- taken from `withName: foo`
         cfg3.getMemory().giga == 8  // <-- taken from `withName: 'flow1:flow2:flow3:bar'`
     }

modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy

@@ -137,8 +137,8 @@ class ParamsDsl2Test extends Dsl2Spec {
         def process = ScriptMeta.get(script).getProcess('alpha'); process.initialize()
 
         then:
-        def inputs = process.processConfig.getInputs()
-        def outputs = process.processConfig.getOutputs()
+        def inputs = process.config.getInputs()
+        def outputs = process.config.getOutputs()
         and:
         inputs.size() == 1
         inputs[0] instanceof StdInParam
@@ -178,8 +178,8 @@ class ParamsDsl2Test extends Dsl2Spec {
         def process = ScriptMeta.get(script).getProcess('beta'); process.initialize()
 
         then:
-        def inputs = process.processConfig.getInputs()
-        def outputs = process.processConfig.getOutputs()
+        def inputs = process.config.getInputs()
+        def outputs = process.config.getOutputs()
         and:
         inputs.size() == 1
         and: