Default values for process inputs

docs/process.md

@@ -800,6 +800,45 @@ In general, multiple input channels should be used to process *combinations* of
 
 See also: {ref}`channel-types`.
 
+(process-input-default-values)=
+
+### Inputs with default values
+
+:::{versionadded} 23.06.0-edge
+:::
+
+Process inputs can be defined with a default value, so that they don't have to be specified when calling the process. Default values are useful for process inputs that aren't always used. For example:
+
+```groovy
+process foo {
+  input:
+    val metadata
+    path ('star/*'), defaultValue: []
+    path ('hisat2/*'), defaultValue: []
+    path ('salmon/*'), defaultValue: []
+  output:
+    stdout
+  script:
+    """
+    echo 'metadata: ${metadata}'
+    [[ -d star ]] && ls star || echo 'skipping star directory'
+    [[ -d hisat2 ]] && ls hisat2 || echo 'skipping hisat2 directory'
+    [[ -d salmon ]] && ls salmon || echo 'skipping salmon directory'
+    """
+}
+
+workflow {
+    metadata = Channel.of('foo')
+    foo(metadata) | view
+}
+```
+
+There are a few important caveats to keep in mind when using default values:
+
+- Inputs with a default value must be declared after inputs without a default value.
+
+- If you provide a value for an input, then you must also provide values for all inputs that precede it, even if those inputs have default values. In the example above, if you wanted to provide a value for the `salmon` input, you would have to provide values for the `star` and `hisat2` inputs as well, regardless of whether you use the default values for those inputs.
+
 (process-output)=
 
 ## Outputs

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

@@ -169,17 +169,27 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
 
         // get params 
         final params = ChannelOut.spread(args)
+
         // sanity check
-        if( params.size() != declaredInputs.size() )
+        if( params.size() > declaredInputs.size() )
             throw new ScriptRuntimeException(missMatchErrMessage(processName, declaredInputs.size(), params.size()))
 
         // set input channels
         for( int i=0; i<params.size(); i++ ) {
-            final inParam = (declaredInputs[i] as BaseInParam)
+            final inParam = (BaseInParam)declaredInputs[i]
             inParam.setFrom(params[i])
             inParam.init()
         }
 
+        for( int i=params.size(); i<declaredInputs.size(); i++ ) {
+            final inParam = (BaseInParam)declaredInputs[i]
+            if( inParam.defaultValue == null )
+                throw new ScriptRuntimeException(missMatchErrMessage(processName, declaredInputs.size(), params.size()))
+
+            inParam.setFrom(CH.value(inParam.defaultValue))
+            inParam.init()
+        }
+
         // set output channels
         // note: the result object must be an array instead of a List to allow process
         // composition ie. to use the process output as the input in another process invocation

modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy

@@ -41,6 +41,8 @@ abstract class BaseInParam extends BaseParam implements InParam {
 
     protected owner
 
+    protected defaultValue
+
     /**
      * The channel to which the input value is bound
      */
@@ -151,6 +153,18 @@ abstract class BaseInParam extends BaseParam implements InParam {
         throw new IllegalArgumentException("Invalid process input definition")
     }
 
+    /**
+     * @return The parameter default value
+     */
+    Object getDefaultValue() {
+        return defaultValue
+    }
+
+    BaseInParam setDefaultValue(Object value) {
+        this.defaultValue = value
+        return this
+    }
+
     BaseInParam bind( Object obj ) {
         this.bindObject = obj
         return this

plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy

@@ -50,8 +50,8 @@ class AwsS3Config {
         this.debug = opts.debug as Boolean
         this.endpoint = opts.endpoint ?: SysEnv.get('AWS_S3_ENDPOINT')
         this.storageClass = parseStorageClass((opts.storageClass ?: opts.uploadStorageClass) as String)     // 'uploadStorageClass' is kept for legacy purposes
-        this.storageEncryption = parseStorageEncryption(opts.storageEncryption as String)
-        this.storageKmsKeyId = opts.storageKmsKeyId
+        this.storageEncryption = parseStorageEncryption(opts.storageEncryption as String) ?: SysEnv.get('NXF_AWS_SSE_MODE')
+        this.storageKmsKeyId = opts.storageKmsKeyId ?: SysEnv.get('NXF_AWS_SSE_KMS_KEY_ID')
         this.pathStyleAccess = opts.s3PathStyleAccess as Boolean
         this.s3Acl = parseS3Acl(opts.s3Acl as String)
     }

plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy

@@ -121,4 +121,18 @@ class AwsS3ConfigTest extends Specification {
         SysEnv.pop()
 
     }
+
+    def 'should set storage encryption via env variable' () {
+        given:
+        SysEnv.push([NXF_AWS_SSE_MODE: 'aws:kms', NXF_AWS_SSE_KMS_KEY_ID: 'xyz1'])
+
+        when:
+        def client = new AwsS3Config([:])
+        then:
+        client.storageKmsKeyId == 'xyz1'
+        client.storageEncryption == 'aws:kms'
+
+        cleanup:
+        SysEnv.pop()
+    }
 }

tests/process-input-default-value.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  input:
+    val metadata
+    path ('star/*'), defaultValue: []
+    path ('hisat2/*'), defaultValue: []
+    path ('salmon/*'), defaultValue: []
+  output:
+    stdout
+  script:
+    """
+    echo 'metadata: ${metadata}'
+    [[ -d star ]] && ls star || echo 'skipping star directory'
+    [[ -d hisat2 ]] && ls hisat2 || echo 'skipping hisat2 directory'
+    [[ -d salmon ]] && ls salmon || echo 'skipping salmon directory'
+    """
+}
+
+workflow {
+    metadata = Channel.of('foo')
+    foo(metadata) | view
+}