feature: emit nullable path in tuples

use nullable instead of allowNull

Signed-off-by: Jorge Aguilera <jorge.aguilera@seqera.io>

Author: jorgeaguileraseqera

docs/process.rst

@@ -632,11 +632,11 @@ section::
 
 
 In the case an input `path` doesn't exist, the process will be aborted. If you want the process will be executed
-independently if the file exists or not, you can set the attribute `allowNull` as true:
+independently if the file exists or not, you can set the attribute `nullable` as true:
 
     process foo {
       input:
-        path x, stageAs: 'data.txt', allowNull:true from '/some/data/file.txt'
+        path x, stageAs: 'data.txt', nullable:true from '/some/data/file.txt'
 
       """
       [[ -f data.txt ]] your_command --in data.txt || other_command
@@ -1082,7 +1082,7 @@ followLinks     When ``true`` target files are return in place of any matching s
 type            Type of paths returned, either ``file``, ``dir`` or ``any`` (default: ``any``, or ``file`` if the specified file name pattern contains a `**` - double star - symbol)
 maxDepth        Maximum number of directory levels to visit (default: `no limit`)
 includeInputs   When ``true`` any input files matching an output file glob pattern are included.
-allowNull       When ``true`` emit a NullablePath instead to abort the process
+nullable       When ``true`` emit a NullablePath instead to abort the process
 ============== =====================
 
 .. warning::

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

@@ -1505,7 +1505,7 @@ class TaskProcessor {
                 def path = param.glob ? splitter.strip(filePattern) : filePattern
                 def file = workDir.resolve(path)
                 def exists = param.followLinks ? file.exists() : file.exists(LinkOption.NOFOLLOW_LINKS)
-                if( !exists && param.allowNull){
+                if( !exists && param.nullable){
                     file = new NullablePath(path)
                     exists = true
                 }
@@ -1695,9 +1695,9 @@ class TaskProcessor {
         return new FileHolder(source, result)
     }
 
-    protected Path normalizeToPath( obj, boolean allowNullable=false ) {
+    protected Path normalizeToPath( obj, boolean nullable=false ) {
 
-        if( obj instanceof NullablePath && !allowNullable)
+        if( obj instanceof NullablePath && !nullable)
             throw new ProcessUnrecoverableException("Path value cannot be null")
 
         if( obj instanceof Path )
@@ -1722,7 +1722,7 @@ class TaskProcessor {
     }
 
     protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch,
-                                                      boolean allowNullable=false ) {
+                                                      boolean nullable=false ) {
 
         Collection allItems = obj instanceof Collection ? obj : [obj]
         def len = allItems.size()
@@ -1732,7 +1732,7 @@ class TaskProcessor {
         for( def item : allItems ) {
 
             if( item instanceof Path || coerceToPath ) {
-                def path = normalizeToPath(item, allowNullable)
+                def path = normalizeToPath(item, nullable)
                 def target = executor.isForeignFile(path) ? batch.addToForeign(path) : path
                 def holder = new FileHolder(target)
                 files << holder
@@ -1946,7 +1946,7 @@ class TaskProcessor {
             final param = entry.getKey()
             final val = entry.getValue()
             final fileParam = param as FileInParam
-            final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch, fileParam.allowNull)
+            final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch, fileParam.nullable)
             final resolved = expandWildcards( fileParam.getFilePattern(ctx), normalized )
             ctx.put( param.name, singleItemOrList(resolved, task.type) )
             count += resolved.size()

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

@@ -35,7 +35,7 @@ class FileInParam extends BaseInParam implements PathQualifier {
 
     private boolean pathQualifier
 
-    private boolean allowNull
+    private boolean nullable
 
     @Override String getTypeName() { pathQualifier ? 'path' : 'file' }
 
@@ -156,12 +156,12 @@ class FileInParam extends BaseInParam implements PathQualifier {
         return this
     }
 
-    FileInParam setAllowNull(boolean value) {
-        this.allowNull = value
+    FileInParam setNullable(boolean value) {
+        this.nullable = value
         return this
     }
 
-    boolean isAllowNull() {
-        return allowNull
+    boolean isNullable() {
+        return nullable
     }
 }

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

@@ -84,7 +84,7 @@ class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, Path
     /**
      * When true, if file doesn't exist, emit a Nullable instead an exception
      */
-    boolean allowNull = false
+    boolean nullable = false
 
     boolean glob = true
 

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

@@ -17,7 +17,7 @@ import test.MockScriptRunner
 @IgnoreIf({System.getenv('NXF_INPUTNULLABLE')})
 class InputNullablePathTest extends Dsl2Spec {
 
-    def 'should fails if allowNull is allowed as output but expected as input'() {
+    def 'should fails if nullable is allowed as output but expected as input'() {
         given:
         def session = new Session( executor: 'nope' ) {
             @Override
@@ -34,7 +34,7 @@ class InputNullablePathTest extends Dsl2Spec {
               input:
                 val id
               output:
-                path("output.txt", allowNull:true)
+                path("output.txt", nullable:true)
               exec:
                 println id
             }

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

@@ -12,7 +12,7 @@ import test.Dsl2Spec
 @IgnoreIf({System.getenv('NXF_INPUTNULLABLE')})
 class OutputNullablePathTest extends Dsl2Spec {
 
-    def 'should fails if allowNull output is not set'() {
+    def 'should fails if nullable output is not set'() {
         given:
         def error = false
         def session = new Session( executor: 'nope' ) {

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

@@ -1152,7 +1152,7 @@ class ParamsOutTest extends Specification {
                 glob: false,
                 optional: false,
                 includeInputs: false,
-                allowNull: true                
+                nullable: true                
                 
               path y, 
                 maxDepth:5,
@@ -1182,7 +1182,7 @@ class ParamsOutTest extends Specification {
         !out0.getGlob()
         !out0.getOptional()
         !out0.getIncludeInputs()
-        out0.isAllowNull()
+        out0.isNullable()
 
         and:
         out1.getMaxDepth() == 5
@@ -1193,7 +1193,7 @@ class ParamsOutTest extends Specification {
         out1.getGlob()
         out1.getOptional()
         out1.getIncludeInputs()
-        !out1.isAllowNull()
+        !out1.isNullable()
     }
 
     def 'should set file options' () {

tests/input-nullablepath-fails.nf

@@ -3,7 +3,7 @@ process test_process1 {
   input:
     val id
   output:
-    path("output.txt", allowNull:true)
+    path("output.txt", nullable:true)
   exec:
     println id
 }