feature: new allowNull attribute in input/output path

add integration test for input and output nullable path

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

Author: jorgeaguileraseqera

Makefile

@@ -74,9 +74,7 @@ refresh:
 #
 test:
 ifndef class
-	./gradlew ${mm}test -PexcludeTests='nextflow.script.OutputNullablePathTest.class,nextflow.script.InputNullablePathTest.class'
-	./gradlew nextflow:test --tests nextflow.script.InputNullablePathTest
-	./gradlew nextflow:test --tests nextflow.script.OutputNullablePathTest
+	./gradlew ${mm}test
 else
 	./gradlew ${mm}test --tests ${class}
 endif

modules/nextflow/build.gradle

@@ -60,9 +60,6 @@ dependencies {
 test {
     minHeapSize = "512m"
     maxHeapSize = "2048m"
-    if (project.hasProperty('excludeTests')) {
-        exclude project.findProperty('excludeTests').split(',')
-    }
 }
 
 application {

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

@@ -1483,13 +1483,13 @@ class TaskProcessor {
 
     protected void collectOutFiles( TaskRun task, FileOutParam param, Path workDir, Map context ) {
 
-        final List<Object> allFiles = []
+        final List<Path> allFiles = []
         // type file parameter can contain a multiple files pattern separating them with a special character
         def entries = param.getFilePatterns(context, task.workDir)
         boolean inputsRemovedFlag = false
         // for each of them collect the produced files
         for( String filePattern : entries ) {
-            List<Object> result = null
+            List<Path> result = null
 
             def splitter = param.glob ? FilePatternSplitter.glob().parse(filePattern) : null
             if( splitter?.isPattern() ) {

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

@@ -14,6 +14,7 @@ import test.MockScriptRunner
  *
  * @author Jorge Aguilera <jorge.aguilera@seqera.io>
  */
+@IgnoreIf({System.getenv('NXF_INPUTNULLABLE')})
 class InputNullablePathTest extends Dsl2Spec {
 
     def 'should fails if allowNull is allowed as output but expected as input'() {

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

@@ -2,17 +2,14 @@ package nextflow.script
 
 
 import nextflow.Session
-import nextflow.exception.MissingFileException
-import nextflow.exception.ProcessUnrecoverableException
 import spock.lang.IgnoreIf
-import spock.lang.Timeout
-import test.BaseSpec
 import test.Dsl2Spec
 
 /**
  *
  * @author Jorge Aguilera <jorge.aguilera@seqera.io>
  */
+@IgnoreIf({System.getenv('NXF_INPUTNULLABLE')})
 class OutputNullablePathTest extends Dsl2Spec {
 
     def 'should fails if allowNull output is not set'() {

tests/checks/input-nullablepath-fails.nf/.checks

@@ -0,0 +1,18 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] && exit 1
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] && exit 1
+
+exit 0

tests/checks/output-nullablepath-fails.nf/.checks

@@ -0,0 +1,18 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] && exit 1
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] && exit 1
+
+exit 0

tests/input-nullablepath-fails.nf

@@ -0,0 +1,23 @@
+nextflow.enable.dsl=2
+process test_process1 {
+  input:
+    val id
+  output:
+    path("output.txt", allowNull:true)
+  exec:
+    println id
+}
+
+process test_process2 {
+  input:
+    path(file)
+  output:
+    val file
+  exec:
+    sleep 1000L
+    println file
+}
+
+workflow {
+    channel.of('foo') | test_process1 | test_process2 |  view()
+}

tests/output-nullablepath-fails.nf

@@ -0,0 +1,13 @@
+nextflow.enable.dsl=2
+
+process test_process1 {
+  input:
+    val id
+  output:
+    path("output.txt")
+  exec:
+    println 'hi'
+}
+workflow {
+    test_process1('foo').out
+}