From 93d04310fcd72319e7af7572df19d73ad633adc8 Mon Sep 17 00:00:00 2001
From: Jorge Aguilera <jorge.aguilera@seqera.io>
Date: Fri, 21 Oct 2022 09:27:27 +0200
Subject: [PATCH 1/6] allow nullables in input/output path

closes #2678

Signed-off-by: Jorge Aguilera <jorge.aguilera@seqera.io>
---
 docs/process.rst                              | 12 ++++++++++
 .../nextflow/processor/TaskProcessor.groovy   | 17 +++++++++++---
 .../nextflow/script/params/FileInParam.groovy | 10 ++++++++
 .../script/params/FileOutParam.groovy         |  5 ++++
 .../groovy/nextflow/util/NullablePath.groovy  | 23 +++++++++++++++++++
 .../script/params/ParamsOutTest.groovy        |  5 +++-
 .../input-nullablepath-fails.nf/.checks       | 18 +++++++++++++++
 .../output-nullablepath-fails.nf/.checks      | 18 +++++++++++++++
 tests/input-nullablepath-fails.nf             | 23 +++++++++++++++++++
 tests/output-nullablepath-fails.nf            | 13 +++++++++++
 10 files changed, 140 insertions(+), 4 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy
 create mode 100644 tests/checks/input-nullablepath-fails.nf/.checks
 create mode 100644 tests/checks/output-nullablepath-fails.nf/.checks
 create mode 100644 tests/input-nullablepath-fails.nf
 create mode 100644 tests/output-nullablepath-fails.nf

diff --git a/docs/process.rst b/docs/process.rst
index d8eed62ecb..15f2496f13 100644
--- a/docs/process.rst
+++ b/docs/process.rst
@@ -537,6 +537,17 @@ section::
       foo('/some/data/file.txt')
     }
 
+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 `nullable` as true:
+
+    process foo {
+      input:
+        path x, stageAs: 'data.txt', nullable:true from '/some/data/file.txt'
+
+      """
+      [[ -f data.txt ]] your_command --in data.txt || other_command
+      """
+    }
 
 Multiple input files
 --------------------
@@ -1004,6 +1015,7 @@ Name                Description
 ``type``            Type of paths returned, either ``file``, ``dir`` or ``any`` (default: ``any``, or ``file`` if the specified file name pattern contains a double star (``**``))
 ``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.
+``nullable``        When ``true`` emit a NullablePath instead to abort the process
 ================== =====================
 
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 80c8fbc778..d28d5cdf70 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -16,6 +16,8 @@
  */
 package nextflow.processor
 
+import nextflow.util.NullablePath
+
 import static nextflow.processor.ErrorStrategy.*
 
 import java.lang.reflect.InvocationTargetException
@@ -1505,6 +1507,10 @@ 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.nullable){
+                    file = new NullablePath(path)
+                    exists = true
+                }
                 if( exists )
                     result = [file]
                 else
@@ -1719,7 +1725,11 @@ class TaskProcessor {
         return new FileHolder(source, result)
     }
 
-    protected Path normalizeToPath( obj ) {
+    protected Path normalizeToPath( obj, boolean nullable=false ) {
+
+        if( obj instanceof NullablePath && !nullable)
+            throw new ProcessUnrecoverableException("Path value cannot be null")
+
         if( obj instanceof Path )
             return obj
 
@@ -1742,7 +1752,8 @@ class TaskProcessor {
         throw new ProcessUnrecoverableException("Not a valid path value: '$str'")
     }
 
-    protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch ) {
+    protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch,
+                                                      boolean nullable=false ) {
 
         Collection allItems = obj instanceof Collection ? obj : [obj]
         def len = allItems.size()
@@ -1752,7 +1763,7 @@ class TaskProcessor {
         for( def item : allItems ) {
 
             if( item instanceof Path || coerceToPath ) {
-                def path = normalizeToPath(item)
+                def path = normalizeToPath(item, nullable)
                 def target = executor.isForeignFile(path) ? batch.addToForeign(path) : path
                 def holder = new FileHolder(target)
                 files << holder
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
index 7148c5ea29..852a69bbca 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -35,6 +35,8 @@ class FileInParam extends BaseInParam implements PathQualifier {
 
     private boolean pathQualifier
 
+    private boolean nullable
+
     @Override String getTypeName() { pathQualifier ? 'path' : 'file' }
 
     @Override String getTypeSimpleName() { getTypeName() + "inparam" }
@@ -154,4 +156,12 @@ class FileInParam extends BaseInParam implements PathQualifier {
         return this
     }
 
+    FileInParam setNullable(boolean value) {
+        this.nullable = value
+        return this
+    }
+
+    boolean isNullable() {
+        return nullable
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
index 50608f6886..98f26c8f51 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -81,6 +81,11 @@ class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, Path
      */
     boolean followLinks = true
 
+    /**
+     * When true, if file doesn't exist, emit a Nullable instead an exception
+     */
+    boolean nullable = false
+
     boolean glob = true
 
     private GString gstring
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy b/modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy
new file mode 100644
index 0000000000..1bfe209fd1
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy
@@ -0,0 +1,23 @@
+package nextflow.util
+
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.PackageScope
+import groovy.util.logging.Slf4j
+import java.nio.file.Path
+
+/**
+ * @author : jorge <jorge.aguilera@seqera.io>
+ *
+ */
+@EqualsAndHashCode
+@Slf4j
+class NullablePath implements Path {
+
+    @PackageScope
+    @Delegate
+    Path delegate
+
+    NullablePath(String path) {
+        delegate = of(path)
+    }
+}
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
index 3d0f034ba4..cd5ae3d821 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
@@ -1151,7 +1151,8 @@ class ParamsOutTest extends Specification {
                 separatorChar: '#',
                 glob: false,
                 optional: false,
-                includeInputs: false
+                includeInputs: false,
+                nullable: true      
                 
               path y, 
                 maxDepth:5,
@@ -1181,6 +1182,7 @@ class ParamsOutTest extends Specification {
         !out0.getGlob()
         !out0.getOptional()
         !out0.getIncludeInputs()
+        out0.isNullable()
 
         and:
         out1.getMaxDepth() == 5
@@ -1191,6 +1193,7 @@ class ParamsOutTest extends Specification {
         out1.getGlob()
         out1.getOptional()
         out1.getIncludeInputs()
+        !out1.isNullable()
     }
 
     def 'should set file options' () {
diff --git a/tests/checks/input-nullablepath-fails.nf/.checks b/tests/checks/input-nullablepath-fails.nf/.checks
new file mode 100644
index 0000000000..346e4a2ea0
--- /dev/null
+++ b/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 
+[[ $? == 0 ]] && exit 1
+
+exit 0
\ No newline at end of file
diff --git a/tests/checks/output-nullablepath-fails.nf/.checks b/tests/checks/output-nullablepath-fails.nf/.checks
new file mode 100644
index 0000000000..346e4a2ea0
--- /dev/null
+++ b/tests/checks/output-nullablepath-fails.nf/.checks
@@ -0,0 +1,18 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] && exit 1
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] && exit 1
+
+exit 0
\ No newline at end of file
diff --git a/tests/input-nullablepath-fails.nf b/tests/input-nullablepath-fails.nf
new file mode 100644
index 0000000000..09c1292e33
--- /dev/null
+++ b/tests/input-nullablepath-fails.nf
@@ -0,0 +1,23 @@
+nextflow.enable.dsl=2
+process test_process1 {
+  input:
+    val id
+  output:
+    path("output.txt", nullable: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()
+}
\ No newline at end of file
diff --git a/tests/output-nullablepath-fails.nf b/tests/output-nullablepath-fails.nf
new file mode 100644
index 0000000000..df93d518e3
--- /dev/null
+++ b/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
+}
\ No newline at end of file

From 199b694f207f622c266ef0accaa3ecdd371fb5bd Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Feb 2023 21:20:16 -0600
Subject: [PATCH 2/6] cleanup

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.rst                              | 16 ++++----
 .../nextflow/processor/TaskProcessor.groovy   | 12 +++---
 .../nextflow/script/params/FileInParam.groovy | 21 +++++-----
 .../script/params/FileOutParam.groovy         |  9 +++--
 .../main/groovy/nextflow/util/NullPath.groovy | 40 +++++++++++++++++++
 .../groovy/nextflow/util/NullablePath.groovy  | 23 -----------
 .../script/params/ParamsOutTest.groovy        | 10 ++---
 7 files changed, 75 insertions(+), 56 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy
 delete mode 100644 modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy

diff --git a/docs/process.rst b/docs/process.rst
index 15f2496f13..1cdfec0909 100644
--- a/docs/process.rst
+++ b/docs/process.rst
@@ -537,16 +537,16 @@ section::
       foo('/some/data/file.txt')
     }
 
-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 `nullable` as true:
+By default, the process will be aborted if an input ``path`` is null. If you want the process
+to be executed even if the path is null, you can set the ``nullable`` attribute to true:
 
     process foo {
-      input:
-        path x, stageAs: 'data.txt', nullable:true from '/some/data/file.txt'
+        input:
+        path(x, stageAs: 'data.txt', nullable: true)
 
-      """
-      [[ -f data.txt ]] your_command --in data.txt || other_command
-      """
+        """
+        [[ -f data.txt ]] your_command --in data.txt || other_command
+        """
     }
 
 Multiple input files
@@ -1015,7 +1015,7 @@ Name                Description
 ``type``            Type of paths returned, either ``file``, ``dir`` or ``any`` (default: ``any``, or ``file`` if the specified file name pattern contains a double star (``**``))
 ``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.
-``nullable``        When ``true`` emit a NullablePath instead to abort the process
+``nullable``        When ``true`` emit ``null`` (instead of aborting) if the output path doesn't exist (default: ``false``)
 ================== =====================
 
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index d28d5cdf70..4a000c7a4a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -16,8 +16,6 @@
  */
 package nextflow.processor
 
-import nextflow.util.NullablePath
-
 import static nextflow.processor.ErrorStrategy.*
 
 import java.lang.reflect.InvocationTargetException
@@ -106,6 +104,7 @@ import nextflow.util.CacheHelper
 import nextflow.util.CollectionHelper
 import nextflow.util.LockManager
 import nextflow.util.LoggerHelper
+import nextflow.util.NullPath
 import org.codehaus.groovy.control.CompilerConfiguration
 import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
 /**
@@ -1507,8 +1506,8 @@ 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.nullable){
-                    file = new NullablePath(path)
+                if( !exists && param.nullable ) {
+                    file = new NullPath(path)
                     exists = true
                 }
                 if( exists )
@@ -1727,7 +1726,7 @@ class TaskProcessor {
 
     protected Path normalizeToPath( obj, boolean nullable=false ) {
 
-        if( obj instanceof NullablePath && !nullable)
+        if( obj instanceof NullPath && !nullable )
             throw new ProcessUnrecoverableException("Path value cannot be null")
 
         if( obj instanceof Path )
@@ -1752,8 +1751,7 @@ class TaskProcessor {
         throw new ProcessUnrecoverableException("Not a valid path value: '$str'")
     }
 
-    protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch,
-                                                      boolean nullable=false ) {
+    protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch, boolean nullable=false ) {
 
         Collection allItems = obj instanceof Collection ? obj : [obj]
         def len = allItems.size()
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
index 852a69bbca..50170a9f8c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -33,10 +33,10 @@ class FileInParam extends BaseInParam implements PathQualifier {
 
     protected filePattern
 
-    private boolean pathQualifier
-
     private boolean nullable
 
+    private boolean pathQualifier
+
     @Override String getTypeName() { pathQualifier ? 'path' : 'file' }
 
     @Override String getTypeSimpleName() { getTypeName() + "inparam" }
@@ -123,6 +123,15 @@ class FileInParam extends BaseInParam implements PathQualifier {
             return value
     }
 
+    FileInParam setNullable(boolean value) {
+        this.nullable = value
+        return this
+    }
+
+    boolean isNullable() {
+        return nullable
+    }
+
     @Override
     FileInParam setPathQualifier(boolean flag) {
         pathQualifier = flag
@@ -156,12 +165,4 @@ class FileInParam extends BaseInParam implements PathQualifier {
         return this
     }
 
-    FileInParam setNullable(boolean value) {
-        this.nullable = value
-        return this
-    }
-
-    boolean isNullable() {
-        return nullable
-    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
index 98f26c8f51..619def68d5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -82,12 +82,15 @@ class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, Path
     boolean followLinks = true
 
     /**
-     * When true, if file doesn't exist, emit a Nullable instead an exception
+     * When true the specified name is interpreted as a glob pattern
      */
-    boolean nullable = false
-
     boolean glob = true
 
+    /**
+     * When true emit null (instead of aborting) if the output path doesn't exist
+     */
+    boolean nullable = false
+
     private GString gstring
     private Closure<String> dynamicObj
     private String filePattern
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy b/modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy
new file mode 100644
index 0000000000..fa9b201df7
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy
@@ -0,0 +1,40 @@
+/*
+ * Copyright 2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.util
+
+import java.nio.file.Path
+
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.PackageScope
+import groovy.util.logging.Slf4j
+
+/**
+ * @author : jorge <jorge.aguilera@seqera.io>
+ *
+ */
+@EqualsAndHashCode
+@Slf4j
+class NullPath implements Path {
+
+    @PackageScope
+    @Delegate
+    Path delegate
+
+    NullPath(String path) {
+        delegate = of(path)
+    }
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy b/modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy
deleted file mode 100644
index 1bfe209fd1..0000000000
--- a/modules/nextflow/src/main/groovy/nextflow/util/NullablePath.groovy
+++ /dev/null
@@ -1,23 +0,0 @@
-package nextflow.util
-
-import groovy.transform.EqualsAndHashCode
-import groovy.transform.PackageScope
-import groovy.util.logging.Slf4j
-import java.nio.file.Path
-
-/**
- * @author : jorge <jorge.aguilera@seqera.io>
- *
- */
-@EqualsAndHashCode
-@Slf4j
-class NullablePath implements Path {
-
-    @PackageScope
-    @Delegate
-    Path delegate
-
-    NullablePath(String path) {
-        delegate = of(path)
-    }
-}
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
index cd5ae3d821..2ce0c7da9b 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
@@ -1151,8 +1151,7 @@ class ParamsOutTest extends Specification {
                 separatorChar: '#',
                 glob: false,
                 optional: false,
-                includeInputs: false,
-                nullable: true      
+                includeInputs: false
                 
               path y, 
                 maxDepth:5,
@@ -1162,7 +1161,8 @@ class ParamsOutTest extends Specification {
                 separatorChar: ':',
                 glob: true,
                 optional: true,
-                includeInputs: true
+                includeInputs: true,
+                nullable: true
 
               return ''
             }
@@ -1182,7 +1182,7 @@ class ParamsOutTest extends Specification {
         !out0.getGlob()
         !out0.getOptional()
         !out0.getIncludeInputs()
-        out0.isNullable()
+        !out0.isNullable()
 
         and:
         out1.getMaxDepth() == 5
@@ -1193,7 +1193,7 @@ class ParamsOutTest extends Specification {
         out1.getGlob()
         out1.getOptional()
         out1.getIncludeInputs()
-        !out1.isNullable()
+        out1.isNullable()
     }
 
     def 'should set file options' () {

From 4e7148edf37fa48d9cfafbd736a4af07d98c1a76 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Feb 2023 21:34:49 -0600
Subject: [PATCH 3/6] Update e2e tests

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy   |  2 +-
 .../.checks                                   |  0
 .../.checks                                   |  0
 .../checks/nullable-path-succeeds.nf/.checks  | 18 ++++++++++++++
 tests/input-nullablepath-fails.nf             | 23 ------------------
 tests/nullable-path-input-fails.nf            | 24 +++++++++++++++++++
 tests/nullable-path-output-fails.nf           | 14 +++++++++++
 tests/nullable-path-succeeds.nf               | 24 +++++++++++++++++++
 tests/output-nullablepath-fails.nf            | 13 ----------
 9 files changed, 81 insertions(+), 37 deletions(-)
 rename tests/checks/{input-nullablepath-fails.nf => nullable-path-input-fails.nf}/.checks (100%)
 rename tests/checks/{output-nullablepath-fails.nf => nullable-path-output-fails.nf}/.checks (100%)
 create mode 100644 tests/checks/nullable-path-succeeds.nf/.checks
 delete mode 100644 tests/input-nullablepath-fails.nf
 create mode 100644 tests/nullable-path-input-fails.nf
 create mode 100644 tests/nullable-path-output-fails.nf
 create mode 100644 tests/nullable-path-succeeds.nf
 delete mode 100644 tests/output-nullablepath-fails.nf

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 4a000c7a4a..60688f0036 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1975,7 +1975,7 @@ class TaskProcessor {
             final param = entry.getKey()
             final val = entry.getValue()
             final fileParam = param as FileInParam
-            final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
+            final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch, fileParam.isNullable())
             final resolved = expandWildcards( fileParam.getFilePattern(ctx), normalized )
             ctx.put( param.name, singleItemOrList(resolved, task.type) )
             count += resolved.size()
diff --git a/tests/checks/input-nullablepath-fails.nf/.checks b/tests/checks/nullable-path-input-fails.nf/.checks
similarity index 100%
rename from tests/checks/input-nullablepath-fails.nf/.checks
rename to tests/checks/nullable-path-input-fails.nf/.checks
diff --git a/tests/checks/output-nullablepath-fails.nf/.checks b/tests/checks/nullable-path-output-fails.nf/.checks
similarity index 100%
rename from tests/checks/output-nullablepath-fails.nf/.checks
rename to tests/checks/nullable-path-output-fails.nf/.checks
diff --git a/tests/checks/nullable-path-succeeds.nf/.checks b/tests/checks/nullable-path-succeeds.nf/.checks
new file mode 100644
index 0000000000..346e4a2ea0
--- /dev/null
+++ b/tests/checks/nullable-path-succeeds.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
\ No newline at end of file
diff --git a/tests/input-nullablepath-fails.nf b/tests/input-nullablepath-fails.nf
deleted file mode 100644
index 09c1292e33..0000000000
--- a/tests/input-nullablepath-fails.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-nextflow.enable.dsl=2
-process test_process1 {
-  input:
-    val id
-  output:
-    path("output.txt", nullable: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()
-}
\ No newline at end of file
diff --git a/tests/nullable-path-input-fails.nf b/tests/nullable-path-input-fails.nf
new file mode 100644
index 0000000000..088838b7c8
--- /dev/null
+++ b/tests/nullable-path-input-fails.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  input:
+    val id
+  output:
+    path('output.txt', nullable: true)
+  exec:
+    println id
+}
+
+process bar {
+  input:
+    path(file)
+  output:
+    val file
+  exec:
+    sleep 1000L
+    println file
+}
+
+workflow {
+    channel.of('foo') | foo | bar | view()
+}
\ No newline at end of file
diff --git a/tests/nullable-path-output-fails.nf b/tests/nullable-path-output-fails.nf
new file mode 100644
index 0000000000..7c6ed2514b
--- /dev/null
+++ b/tests/nullable-path-output-fails.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  input:
+    val id
+  output:
+    path('output.txt')
+  exec:
+    println 'hi'
+}
+
+workflow {
+    foo('foo')
+}
\ No newline at end of file
diff --git a/tests/nullable-path-succeeds.nf b/tests/nullable-path-succeeds.nf
new file mode 100644
index 0000000000..16a3c3c3cd
--- /dev/null
+++ b/tests/nullable-path-succeeds.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  input:
+    val id
+  output:
+    path('output.txt', nullable: true)
+  exec:
+    println id
+}
+
+process bar {
+  input:
+    path(file, nullable: true)
+  output:
+    val file
+  exec:
+    sleep 1000L
+    println file
+}
+
+workflow {
+    channel.of('foo') | foo | bar | view()
+}
\ No newline at end of file
diff --git a/tests/output-nullablepath-fails.nf b/tests/output-nullablepath-fails.nf
deleted file mode 100644
index df93d518e3..0000000000
--- a/tests/output-nullablepath-fails.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-nextflow.enable.dsl=2
-
-process test_process1 {
-  input:
-    val id
-  output:
-    path("output.txt")
-  exec:
-    println 'hi'
-}
-workflow {
-    test_process1('foo').out
-}
\ No newline at end of file

From ff8ecc96a55861c1a4fba957d061751d1a1b6b99 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Feb 2023 21:42:34 -0600
Subject: [PATCH 4/6] Add tuples to nullable path e2e tests

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 tests/nullable-path-input-fails.nf  | 4 ++--
 tests/nullable-path-output-fails.nf | 2 +-
 tests/nullable-path-succeeds.nf     | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/nullable-path-input-fails.nf b/tests/nullable-path-input-fails.nf
index 088838b7c8..aad3dde4ff 100644
--- a/tests/nullable-path-input-fails.nf
+++ b/tests/nullable-path-input-fails.nf
@@ -4,14 +4,14 @@ process foo {
   input:
     val id
   output:
-    path('output.txt', nullable: true)
+    tuple val(id), path('output.txt', nullable: true)
   exec:
     println id
 }
 
 process bar {
   input:
-    path(file)
+    tuple val(id), path(file)
   output:
     val file
   exec:
diff --git a/tests/nullable-path-output-fails.nf b/tests/nullable-path-output-fails.nf
index 7c6ed2514b..e3cd052084 100644
--- a/tests/nullable-path-output-fails.nf
+++ b/tests/nullable-path-output-fails.nf
@@ -4,7 +4,7 @@ process foo {
   input:
     val id
   output:
-    path('output.txt')
+    tuple val(id), path('output.txt')
   exec:
     println 'hi'
 }
diff --git a/tests/nullable-path-succeeds.nf b/tests/nullable-path-succeeds.nf
index 16a3c3c3cd..afadb4a1f5 100644
--- a/tests/nullable-path-succeeds.nf
+++ b/tests/nullable-path-succeeds.nf
@@ -4,14 +4,14 @@ process foo {
   input:
     val id
   output:
-    path('output.txt', nullable: true)
+    tuple val(id), path('output.txt', nullable: true)
   exec:
     println id
 }
 
 process bar {
   input:
-    path(file, nullable: true)
+    tuple val(id), path(file, nullable: true)
   output:
     val file
   exec:

From 26cc4290f7ddaf2e9f8b64c1924f6a58d02e15ea Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 22 Feb 2023 03:24:33 -0600
Subject: [PATCH 5/6] Fix integration test

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 tests/checks/nullable-path-succeeds.nf/.checks | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/checks/nullable-path-succeeds.nf/.checks b/tests/checks/nullable-path-succeeds.nf/.checks
index 346e4a2ea0..5c332305d9 100644
--- a/tests/checks/nullable-path-succeeds.nf/.checks
+++ b/tests/checks/nullable-path-succeeds.nf/.checks
@@ -5,7 +5,7 @@ set +e
 #
 echo ''
 $NXF_RUN 
-[[ $? == 0 ]] && exit 1
+[[ $? == 0 ]] || false
 
 
 #
@@ -13,6 +13,4 @@ $NXF_RUN
 #
 echo ''
 $NXF_RUN -resume 
-[[ $? == 0 ]] && exit 1
-
-exit 0
\ No newline at end of file
+[[ $? == 0 ]] || false

From 19209212cf2bdf53794953b89210e554e3ce50a6 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Fri, 24 Feb 2023 14:43:12 -0600
Subject: [PATCH 6/6] Add note about optional vs nullable [ci skip]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.rst | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docs/process.rst b/docs/process.rst
index c60d02e09d..a662b6c283 100644
--- a/docs/process.rst
+++ b/docs/process.rst
@@ -1265,6 +1265,11 @@ In this example, the process is normally expected to produce an ``output.txt`` f
 cases where the file is legitimately missing, the process does not fail. The output channel will
 only contain values for those processes that produce ``output.txt``.
 
+.. note::
+    Path outputs can also be defined as ``nullable``. Whereas an ``optional`` path will emit nothing
+    if the output file does not exist, a ``nullable`` path will emit a "null" path that can trigger
+    downstream computations, such as a process that has a ``nullable`` path input.
+
 
 When
 ====