From c6d4950a603e2b4da0113789158068a541be1fd4 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 1 Mar 2023 11:59:59 -0600
Subject: [PATCH 01/16] Add arity option for path inputs and outputs

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.rst                              | 46 +++++++++++-
 .../nextflow/processor/TaskProcessor.groovy   | 28 ++++---
 .../nextflow/script/params/ArityParam.groovy  | 74 +++++++++++++++++++
 .../nextflow/script/params/FileInParam.groovy | 13 +++-
 .../script/params/FileOutParam.groovy         | 13 +++-
 tests/process-arity.nf                        | 37 ++++++++++
 6 files changed, 197 insertions(+), 14 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
 create mode 100644 tests/process-arity.nf

diff --git a/docs/process.rst b/docs/process.rst
index cd40d5d31b..4f12e2a24e 100644
--- a/docs/process.rst
+++ b/docs/process.rst
@@ -582,10 +582,10 @@ will output::
 
 The target input file name may contain the ``*`` and ``?`` wildcards, which can be used
 to control the name of staged files. The following table shows how the wildcards are
-replaced depending on the cardinality of the received input collection.
+replaced depending on the arity of the received input collection.
 
 ============ ============== ==================================================
-Cardinality   Name pattern   Staged file names
+Arity        Name pattern   Staged file names
 ============ ============== ==================================================
  any         ``*``           named as the source file
  1           ``file*.ext``   ``file.ext``
@@ -650,6 +650,26 @@ with the current execution context.
   and some of these files may have the same filename. In this case, a solution would be to use
   the option ``stageAs``.
 
+
+Input file arity
+----------------
+
+.. note::
+  This feature requires Nextflow version 23.04.0 or later.
+
+The *arity* of a ``path`` input is the number of files that it is expected to contain. The arity can be a
+number or a range. Here are some examples::
+
+    input:
+        path('one.txt', arity: '1')         // exactly one file is expected
+        path('pair_*.txt', arity: '2')      // exactly two files are expected
+        path('many_*.txt', arity: '1..*')   // one or more files are expected
+        path('optional.txt', arity: '0..1') // zero or one file is expected
+
+When a task is created, Nextflow will check whether the received files for each path input match the
+declared arity, and fail if they do not. The default arity is ``'1..*'``.
+
+
 Input type ``env``
 ------------------
 
@@ -1145,6 +1165,28 @@ on the actual value of the ``species`` input.
   because it will result in simpler and more portable code.
 
 
+Output file arity
+-----------------
+
+.. note::
+  This feature requires Nextflow version 23.04.0 or later.
+
+The *arity* of a ``path`` output is the number of files that it is expected to contain. The arity can be a
+number or a range. Here are some examples::
+
+    output:
+        path('one.txt', arity: '1')         // exactly one file is expected
+        path('pair_*.txt', arity: '2')      // exactly two files are expected
+        path('many_*.txt', arity: '1..*')   // one or more files are expected
+        path('optional.txt', arity: '0..1') // zero or one file is expected (equivalent to optional: true)
+
+When a task completes, Nextflow will check whether the produced files for each path output match the
+declared arity, and fail if they do not.
+
+The default arity is ``'1..*'``, or ``'0..*'`` if the output is declared optional. If you declare an
+output as optional and also give it an arity, the optional flag will be ignored.
+
+
 .. _process-env:
 
 Output type ``env``
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 5c44c6153d..3e2dd1ede7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1565,7 +1565,7 @@ class TaskProcessor {
             if( result )
                 allFiles.addAll(result)
 
-            else if( !param.optional ) {
+            else if( param.arity.min > 0 ) {
                 def msg = "Missing output file(s) `$filePattern` expected by process `${safeTaskName(task)}`"
                 if( inputsRemovedFlag )
                     msg += " (note: input files are not included in the default matching set)"
@@ -1573,7 +1573,10 @@ class TaskProcessor {
             }
         }
 
-        task.setOutput( param, allFiles.size()==1 ? allFiles[0] : allFiles )
+        if( !param.arity.contains(allFiles.size()) )
+            throw new IllegalArgumentException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
+
+        task.setOutput( param, param.arity.isSingle() ? allFiles[0] : allFiles )
 
     }
 
@@ -1816,10 +1819,10 @@ class TaskProcessor {
         return files
     }
 
-    protected singleItemOrList( List<FileHolder> items, ScriptType type ) {
+    protected singleItemOrList( List<FileHolder> items, boolean isSingle, ScriptType type ) {
         assert items != null
 
-        if( items.size() == 1 ) {
+        if( isSingle ) {
             return makePath(items[0],type)
         }
 
@@ -2017,17 +2020,22 @@ class TaskProcessor {
             final param = entry.getKey()
             final val = entry.getValue()
             final fileParam = param as FileInParam
-            final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
-            final resolved = expandWildcards( fileParam.getFilePattern(ctx), normalized )
-            ctx.put( param.name, singleItemOrList(resolved, task.type) )
-            count += resolved.size()
-            for( FileHolder item : resolved ) {
+
+            def files = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
+            files = expandWildcards( fileParam.getFilePattern(ctx), files )
+
+            if( !param.arity.contains(files.size()) )
+                throw new IllegalArgumentException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${files.size()}")
+
+            ctx.put( param.name, singleItemOrList(files, param.arity.isSingle(), task.type) )
+            count += files.size()
+            for( FileHolder item : files ) {
                 Integer num = allNames.getOrCreate(item.stageName, 0) +1
                 allNames.put(item.stageName,num)
             }
 
             // add the value to the task instance context
-            task.setInput(param, resolved)
+            task.setInput(param, files)
         }
 
         // -- set the delegate map as context in the task config
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
new file mode 100644
index 0000000000..9ca39380d7
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -0,0 +1,74 @@
+/*
+ * 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.script.params
+
+
+/**
+ * Implements an arity option for process inputs and outputs.
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+trait ArityParam {
+
+    private Range arity = null
+
+    def setArity(String arity) {
+        if( arity.isInteger() ) {
+            def n = arity.toInteger()
+            this.arity = new Range(n, n)
+        }
+        else if( arity.contains('..') && arity.tokenize('..').size() == 2 ) {
+            def (min, max) = arity.tokenize('..')
+            this.arity = new Range(
+                min == '*' ? 0 : min.toInteger(),
+                max == '*' ? Integer.MAX_VALUE : max.toInteger()
+            )
+        }
+        else {
+            throw new IllegalArgumentException("Output path arity should be a number (e.g. '1') or range (e.g. '1..*')")
+        }
+        return this
+    }
+
+    Range getArity() {
+        arity
+    }
+
+    static class Range {
+        int min
+        int max
+
+        Range(int min, int max) {
+            this.min = min
+            this.max = max
+        }
+
+        boolean contains(int value) {
+            min <= value && value <= max
+        }
+
+        boolean isSingle() {
+            min == 1 && max == 1
+        }
+
+        @Override
+        String toString() {
+            "${min}..${max == Integer.MAX_VALUE ? '*' : max}".toString()
+        }
+    }
+
+}
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..285092ef66 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -29,7 +29,7 @@ import nextflow.script.TokenVar
  */
 @Slf4j
 @InheritConstructors
-class FileInParam extends BaseInParam implements PathQualifier {
+class FileInParam extends BaseInParam implements ArityParam, PathQualifier {
 
     protected filePattern
 
@@ -121,6 +121,17 @@ class FileInParam extends BaseInParam implements PathQualifier {
             return value
     }
 
+    /**
+     * Override to initialize arity with default value.
+     */
+    @Override
+    Range getArity() {
+        if( ArityParam.super.getArity() == null )
+            ArityParam.super.setArity('1..*')
+
+        ArityParam.super.getArity()
+    }
+
     @Override
     FileInParam setPathQualifier(boolean flag) {
         pathQualifier = flag
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..3cf5607b69 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -34,7 +34,7 @@ import nextflow.util.BlankSeparatedList
  */
 @Slf4j
 @InheritConstructors
-class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, PathQualifier {
+class FileOutParam extends BaseOutParam implements OutParam, ArityParam, OptionalParam, PathQualifier {
 
     /**
      * ONLY FOR TESTING DO NOT USE
@@ -262,6 +262,17 @@ class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, Path
         return nameObj ? super.getName() : null
     }
 
+    /**
+     * Override to initialize arity with default value based on optional.
+     */
+    @Override
+    Range getArity() {
+        if( ArityParam.super.getArity() == null )
+            ArityParam.super.setArity( optional ? '0..*' : '1..*' )
+
+        ArityParam.super.getArity()
+    }
+
     @Override
     FileOutParam setPathQualifier(boolean flag) {
         pathQualifier = flag
diff --git a/tests/process-arity.nf b/tests/process-arity.nf
new file mode 100644
index 0000000000..1fa121ce60
--- /dev/null
+++ b/tests/process-arity.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  output:
+    path('one.txt', arity: '1')
+    path('pair_*.txt', arity: '2')
+    path('many_*.txt', arity: '1..*')
+    path('optional.txt', arity: '0..1')
+  script:
+    """
+    echo 'one' > one.txt
+    echo 'pair_1' > pair_1.txt
+    echo 'pair_2' > pair_2.txt
+    echo 'many_1' > many_1.txt
+    echo 'many_2' > many_2.txt
+    echo 'many_3' > many_3.txt
+    """
+}
+
+process bar {
+  input:
+    path('one.txt', arity: '1')
+    path('pair_*.txt', arity: '2')
+    path('many_*.txt', arity: '1..*')
+    path('optional.txt', arity: '0..1')
+  script:
+    """
+    cat one.txt
+    cat pair_*.txt
+    cat many_*.txt
+    [[ -f optional.txt ]] && cat optional.txt || true
+    """
+}
+
+workflow {
+    foo | bar
+}
\ No newline at end of file

From 9a16f0108c1e0357e72ad6f66e7f55150e54e2f9 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 2 Mar 2023 17:46:48 -0600
Subject: [PATCH 02/16] Change default arity to depend on file pattern

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../groovy/nextflow/processor/TaskProcessor.groovy     |  6 +++---
 .../groovy/nextflow/script/params/FileInParam.groovy   |  6 +++++-
 .../groovy/nextflow/script/params/FileOutParam.groovy  |  6 +++++-
 .../groovy/nextflow/processor/TaskProcessorTest.groovy | 10 ++++++++--
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 3e2dd1ede7..00e093e004 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1576,7 +1576,7 @@ class TaskProcessor {
         if( !param.arity.contains(allFiles.size()) )
             throw new IllegalArgumentException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
 
-        task.setOutput( param, param.arity.isSingle() ? allFiles[0] : allFiles )
+        task.setOutput( param, allFiles.size()==1 && param.arity.isSingle() ? allFiles[0] : allFiles )
 
     }
 
@@ -1819,10 +1819,10 @@ class TaskProcessor {
         return files
     }
 
-    protected singleItemOrList( List<FileHolder> items, boolean isSingle, ScriptType type ) {
+    protected singleItemOrList( List<FileHolder> items, boolean single, ScriptType type ) {
         assert items != null
 
-        if( isSingle ) {
+        if( items.size() == 1 && single ) {
             return makePath(items[0],type)
         }
 
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 285092ef66..c2be4a9468 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -127,7 +127,11 @@ class FileInParam extends BaseInParam implements ArityParam, PathQualifier {
     @Override
     Range getArity() {
         if( ArityParam.super.getArity() == null )
-            ArityParam.super.setArity('1..*')
+            ArityParam.super.setArity(
+                filePattern?.contains('*') || filePattern?.contains('?')
+                    ? '1..*'
+                    : '1'
+            )
 
         ArityParam.super.getArity()
     }
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 3cf5607b69..0573bfb54f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -268,7 +268,11 @@ class FileOutParam extends BaseOutParam implements OutParam, ArityParam, Optiona
     @Override
     Range getArity() {
         if( ArityParam.super.getArity() == null )
-            ArityParam.super.setArity( optional ? '0..*' : '1..*' )
+            ArityParam.super.setArity(
+                filePattern?.contains('*') || filePattern?.contains('?')
+                    ? optional ? '0..*' : '1..*'
+                    : optional ? '0..1' : '1'
+            )
 
         ArityParam.super.getArity()
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index 879e51f381..5386a871da 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -186,13 +186,19 @@ class TaskProcessorTest extends Specification {
 
         when:
         def list = [ FileHolder.get(path1, 'x_file_1') ]
-        def result = processor.singleItemOrList(list, ScriptType.SCRIPTLET)
+        def result = processor.singleItemOrList(list, true, ScriptType.SCRIPTLET)
         then:
         result.toString() == 'x_file_1'
 
+        when:
+        list = [ FileHolder.get(path1, 'x_file_1') ]
+        result = processor.singleItemOrList(list, false, ScriptType.SCRIPTLET)
+        then:
+        result*.toString() == ['x_file_1']
+
         when:
         list = [ FileHolder.get(path1, 'x_file_1'), FileHolder.get(path2, 'x_file_2'), FileHolder.get(path3, 'x_file_3') ]
-        result = processor.singleItemOrList(list, ScriptType.SCRIPTLET)
+        result = processor.singleItemOrList(list, false, ScriptType.SCRIPTLET)
         then:
         result*.toString() == [ 'x_file_1',  'x_file_2',  'x_file_3']
 

From 4738a972f8989d7b048f8e61f5a63bf7b7d7310b Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 2 Mar 2023 17:58:44 -0600
Subject: [PATCH 03/16] Change arity "single"-ness to include optional single
 (`0..1`)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/script/params/ArityParam.groovy    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index 9ca39380d7..6fdd8ea26e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -62,7 +62,7 @@ trait ArityParam {
         }
 
         boolean isSingle() {
-            min == 1 && max == 1
+            max == 1
         }
 
         @Override

From 058474f16214c54ad5b0c418e28b01f0045296f1 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 8 Mar 2023 15:53:11 -0600
Subject: [PATCH 04/16] Remove default arity, use original behavior if arity
 not specified

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy       | 10 +++++-----
 .../nextflow/script/params/FileInParam.groovy     | 15 ---------------
 .../nextflow/script/params/FileOutParam.groovy    | 15 ---------------
 3 files changed, 5 insertions(+), 35 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 00e093e004..75c92cea8d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1565,7 +1565,7 @@ class TaskProcessor {
             if( result )
                 allFiles.addAll(result)
 
-            else if( param.arity.min > 0 ) {
+            else if( !param.optional && (!param.arity || param.arity.min > 0) ) {
                 def msg = "Missing output file(s) `$filePattern` expected by process `${safeTaskName(task)}`"
                 if( inputsRemovedFlag )
                     msg += " (note: input files are not included in the default matching set)"
@@ -1573,10 +1573,10 @@ class TaskProcessor {
             }
         }
 
-        if( !param.arity.contains(allFiles.size()) )
+        if( param.arity && !param.arity.contains(allFiles.size()) )
             throw new IllegalArgumentException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
 
-        task.setOutput( param, allFiles.size()==1 && param.arity.isSingle() ? allFiles[0] : allFiles )
+        task.setOutput( param, allFiles.size()==1 && (!param.arity || param.arity.isSingle()) ? allFiles[0] : allFiles )
 
     }
 
@@ -2024,10 +2024,10 @@ class TaskProcessor {
             def files = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
             files = expandWildcards( fileParam.getFilePattern(ctx), files )
 
-            if( !param.arity.contains(files.size()) )
+            if( param.arity && !param.arity.contains(files.size()) )
                 throw new IllegalArgumentException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${files.size()}")
 
-            ctx.put( param.name, singleItemOrList(files, param.arity.isSingle(), task.type) )
+            ctx.put( param.name, singleItemOrList(files, !param.arity || param.arity.isSingle(), task.type) )
             count += files.size()
             for( FileHolder item : files ) {
                 Integer num = allNames.getOrCreate(item.stageName, 0) +1
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 c2be4a9468..ed984ff12b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -121,21 +121,6 @@ class FileInParam extends BaseInParam implements ArityParam, PathQualifier {
             return value
     }
 
-    /**
-     * Override to initialize arity with default value.
-     */
-    @Override
-    Range getArity() {
-        if( ArityParam.super.getArity() == null )
-            ArityParam.super.setArity(
-                filePattern?.contains('*') || filePattern?.contains('?')
-                    ? '1..*'
-                    : '1'
-            )
-
-        ArityParam.super.getArity()
-    }
-
     @Override
     FileInParam setPathQualifier(boolean flag) {
         pathQualifier = flag
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 0573bfb54f..e6a46ea273 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -262,21 +262,6 @@ class FileOutParam extends BaseOutParam implements OutParam, ArityParam, Optiona
         return nameObj ? super.getName() : null
     }
 
-    /**
-     * Override to initialize arity with default value based on optional.
-     */
-    @Override
-    Range getArity() {
-        if( ArityParam.super.getArity() == null )
-            ArityParam.super.setArity(
-                filePattern?.contains('*') || filePattern?.contains('?')
-                    ? optional ? '0..*' : '1..*'
-                    : optional ? '0..1' : '1'
-            )
-
-        ArityParam.super.getArity()
-    }
-
     @Override
     FileOutParam setPathQualifier(boolean flag) {
         pathQualifier = flag

From 2a015c726c4a8baeb14576f927356b977dd59743 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 8 Mar 2023 16:59:14 -0600
Subject: [PATCH 05/16] Add ArityParam unit test

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/script/params/ArityParam.groovy  | 39 +++++++++-------
 .../script/params/ArityParamTest.groovy       | 44 +++++++++++++++++++
 2 files changed, 66 insertions(+), 17 deletions(-)
 create mode 100644 modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index 6fdd8ea26e..a4a2e3df5b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -16,36 +16,41 @@
 
 package nextflow.script.params
 
+import groovy.transform.CompileStatic
 
 /**
  * Implements an arity option for process inputs and outputs.
  *
  * @author Ben Sherman <bentshermann@gmail.com>
  */
+@CompileStatic
 trait ArityParam {
 
-    private Range arity = null
+    Range arity
 
-    def setArity(String arity) {
-        if( arity.isInteger() ) {
-            def n = arity.toInteger()
+    Range getArity() { arity }
+
+    def setArity(String value) {
+        if( value.isInteger() ) {
+            def n = value.toInteger()
             this.arity = new Range(n, n)
+            return this
         }
-        else if( arity.contains('..') && arity.tokenize('..').size() == 2 ) {
-            def (min, max) = arity.tokenize('..')
-            this.arity = new Range(
-                min == '*' ? 0 : min.toInteger(),
-                max == '*' ? Integer.MAX_VALUE : max.toInteger()
-            )
-        }
-        else {
-            throw new IllegalArgumentException("Output path arity should be a number (e.g. '1') or range (e.g. '1..*')")
+
+        def tokens = value.tokenize('..')
+        if( tokens.size() == 2 ) {
+            def min = tokens[0]
+            def max = tokens[1]
+            if( min.isInteger() && (max == '*' || max.isInteger()) ) {
+                this.arity = new Range(
+                    min.toInteger(),
+                    max == '*' ? Integer.MAX_VALUE : max.toInteger()
+                )
+                return this
+            }
         }
-        return this
-    }
 
-    Range getArity() {
-        arity
+        throw new IllegalArgumentException("Path arity should be a number (e.g. '1') or a range (e.g. '1..*')")
     }
 
     static class Range {
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
new file mode 100644
index 0000000000..284d548e44
--- /dev/null
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
@@ -0,0 +1,44 @@
+/*
+ * 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.script.params
+
+import spock.lang.Specification
+import spock.lang.Unroll
+/**
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+class ArityParamTest extends Specification {
+
+    @Unroll
+    def 'should set arity' () {
+
+        when:
+        def param = [:] as ArityParam
+        param.setArity(VALUE)
+        then:
+        param.arity.min == MIN
+        param.arity.max == MAX
+
+        where:
+        VALUE  | MIN | MAX
+        '1'    | 1   | 1
+        '0..1' | 0   | 1
+        '1..*' | 1   | Integer.MAX_VALUE
+    }
+
+}

From 4e17c9972b2d60ee316ab3820192fe40545784e7 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 9 Mar 2023 09:48:29 -0600
Subject: [PATCH 06/16] Add tests for ArityParam (currently failing)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/script/params/ArityParam.groovy  |  4 ++-
 .../script/params/ArityParamTest.groovy       | 25 +++++++++++++++++--
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index a4a2e3df5b..282cc6a888 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -72,7 +72,9 @@ trait ArityParam {
 
         @Override
         String toString() {
-            "${min}..${max == Integer.MAX_VALUE ? '*' : max}".toString()
+            min == max
+                ? min.toString()
+                : "${min}..${max == Integer.MAX_VALUE ? '*' : max}".toString()
         }
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
index 284d548e44..4104ba15f0 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
@@ -24,11 +24,15 @@ import spock.lang.Unroll
  */
 class ArityParamTest extends Specification {
 
+    static class DefaultArityParam implements ArityParam {
+        DefaultArityParam() {}
+    }
+
     @Unroll
-    def 'should set arity' () {
+    def testArity () {
 
         when:
-        def param = [:] as ArityParam
+        def param = new DefaultArityParam()
         param.setArity(VALUE)
         then:
         param.arity.min == MIN
@@ -41,4 +45,21 @@ class ArityParamTest extends Specification {
         '1..*' | 1   | Integer.MAX_VALUE
     }
 
+    @Unroll
+    def testArityRange () {
+
+        when:
+        def range = new ArityParam.Range(MIN, MAX)
+        then:
+        range.contains(2) == TWO
+        range.isSingle() == SINGLE
+        range.toString() == STRING
+
+        where:
+        MIN | MAX               | TWO   | SINGLE | STRING
+        1   | 1                 | false | true   | '1'
+        0   | 1                 | false | true   | '0..1'
+        1   | Integer.MAX_VALUE | true  | false  | '1..*'
+    }
+
 }

From 8c5e93cbec1eada1f6bc6e134aa8d2874380678a Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 30 Mar 2023 10:56:48 -0500
Subject: [PATCH 07/16] Add arity to params unit tests

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../groovy/nextflow/script/params/ArityParam.groovy   |  5 +++++
 .../groovy/nextflow/script/params/ParamsInTest.groovy | 11 +++++++----
 .../nextflow/script/params/ParamsOutTest.groovy       |  8 ++++++--
 3 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index 282cc6a888..3d81eb1979 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -70,6 +70,11 @@ trait ArityParam {
             max == 1
         }
 
+        @Override
+        boolean equals(Object obj) {
+            min == obj.min && max == obj.max
+        }
+
         @Override
         String toString() {
             min == max
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
index e2ef5258ce..c96d223f16 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
@@ -706,12 +706,12 @@ class ParamsInTest extends Dsl2Spec {
 
             process hola {
               input:
-              path x
-              path f1
-              path '*.fa' 
+              path x, arity: '1'
+              path f1, arity: '1..2'
+              path '*.fa', arity: '1..*'
               path 'file.txt'
               path f2, name: '*.fa'
-              path f3, stageAs: '*.txt' 
+              path f3, stageAs: '*.txt'
 
               return ''
             }
@@ -737,18 +737,21 @@ class ParamsInTest extends Dsl2Spec {
         in0.inChannel.val == FILE
         in0.index == 0
         in0.isPathQualifier()
+        in0.arity == new ArityParam.Range(1, 1)
 
         in1.name == 'f1'
         in1.filePattern == '*'
         in1.inChannel.val == FILE
         in1.index == 1
         in1.isPathQualifier()
+        in1.arity == new ArityParam.Range(1, 2)
 
         in2.name == '*.fa'
         in2.filePattern == '*.fa'
         in2.inChannel.val == FILE
         in2.index == 2
         in2.isPathQualifier()
+        in2.arity == new ArityParam.Range(1, Integer.MAX_VALUE)
 
         in3.name == 'file.txt'
         in3.filePattern == 'file.txt'
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 1c46c898ba..d19820f4f6 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
@@ -931,7 +931,8 @@ class ParamsOutTest extends Dsl2Spec {
                 separatorChar: '#',
                 glob: false,
                 optional: false,
-                includeInputs: false
+                includeInputs: false,
+                arity: '1'
                 
               path y, 
                 maxDepth:5,
@@ -941,7 +942,8 @@ class ParamsOutTest extends Dsl2Spec {
                 separatorChar: ':',
                 glob: true,
                 optional: true,
-                includeInputs: true
+                includeInputs: true,
+                arity: '0..*'
 
               return ''
             }
@@ -963,6 +965,7 @@ class ParamsOutTest extends Dsl2Spec {
         !out0.getGlob()
         !out0.getOptional()
         !out0.getIncludeInputs()
+        out0.getArity() == new ArityParam.Range(1, 1)
 
         and:
         out1.getMaxDepth() == 5
@@ -973,6 +976,7 @@ class ParamsOutTest extends Dsl2Spec {
         out1.getGlob()
         out1.getOptional()
         out1.getIncludeInputs()
+        out1.getArity() == new ArityParam.Range(0, Integer.MAX_VALUE)
     }
 
     def 'should set file options' () {

From 04fbb86abd2af19122a8f05bc05a162cb82e210a Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Fri, 21 Apr 2023 11:24:15 -0500
Subject: [PATCH 08/16] Fix liftbot warning

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../main/groovy/nextflow/script/params/ArityParam.groovy   | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index 3d81eb1979..f259934854 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -17,6 +17,7 @@
 package nextflow.script.params
 
 import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
 
 /**
  * Implements an arity option for process inputs and outputs.
@@ -53,6 +54,7 @@ trait ArityParam {
         throw new IllegalArgumentException("Path arity should be a number (e.g. '1') or a range (e.g. '1..*')")
     }
 
+    @EqualsAndHashCode
     static class Range {
         int min
         int max
@@ -70,11 +72,6 @@ trait ArityParam {
             max == 1
         }
 
-        @Override
-        boolean equals(Object obj) {
-            min == obj.min && max == obj.max
-        }
-
         @Override
         String toString() {
             min == max

From 7ec397fd262ce0186603cae6f7921966c9e44d55 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 24 May 2023 17:53:40 +0200
Subject: [PATCH 09/16] Add support for AWS SSE env variables

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/cloud/aws/config/AwsS3Config.groovy   |  4 ++--
 .../cloud/aws/config/AwsS3ConfigTest.groovy        | 14 ++++++++++++++
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
index e479925314..5ff28aac75 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
+++ b/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)
     }
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
index 116a64456b..0f5cd1f643 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
+++ b/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()
+    }
 }

From bbdca3ebb8d89a94e2c6cfa8a8fb9226af3a576e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 15 Aug 2023 20:54:13 +0200
Subject: [PATCH 10/16] Update docs [ci skip]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/process.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/process.md b/docs/process.md
index 9f4aec015c..bd4db434a4 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -474,7 +474,7 @@ workflow {
 Available options:
 
 `arity`
-: :::{versionadded} 23.06.0-edge
+: :::{versionadded} 23.09.0-edge
   :::
 : Specify the number of expected files (default: `'1..*'`). Can be a number or a range:
 
@@ -933,7 +933,7 @@ In the above example, the `randomNum` process creates a file named `result.txt`
 Available options:
 
 `arity`
-: :::{versionadded} 23.06.0-edge
+: :::{versionadded} 23.09.0-edge
   :::
 : Specify the number of expected files (default: ``'1..*'``, or ``'0..*'`` if the output is declared optional). Can be a number or a range:
 

From 88da8bb46a80969b6cfa41ca9903d9def2007840 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 15 Aug 2023 18:15:37 -0500
Subject: [PATCH 11/16] Add nullable inputs/outputs and other improvements

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md                               | 16 ++++++----
 .../nextflow/processor/TaskProcessor.groovy   | 32 +++++++++++--------
 .../nextflow/script/params/ArityParam.groovy  | 22 ++++++++++---
 .../script/params/ArityParamTest.groovy       | 20 ++++++------
 .../cloud/aws/config/AwsS3Config.groovy       |  4 +--
 .../cloud/aws/config/AwsS3ConfigTest.groovy   | 14 --------
 tests/process-arity.nf                        |  6 ++--
 7 files changed, 61 insertions(+), 53 deletions(-)

diff --git a/docs/process.md b/docs/process.md
index bd4db434a4..cfd6a3d317 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -476,7 +476,7 @@ Available options:
 `arity`
 : :::{versionadded} 23.09.0-edge
   :::
-: Specify the number of expected files (default: `'1..*'`). Can be a number or a range:
+: Specify the number of expected files. Can be a number or a range:
 
   ```groovy
   input:
@@ -488,6 +488,8 @@ Available options:
 
   When a task is created, Nextflow will check whether the received files for each path input match the declared arity, and fail if they do not.
 
+  An input is *nullable* if the arity is exactly `0..1`. Nullable inputs can accept "null" files from nullable `path` outputs.
+
 `stageAs`
 : Specify how the file should be named in the task work directory:
 
@@ -536,9 +538,9 @@ seq1 seq2 seq3
 ...
 ```
 
-The target input file name may contain the `*` and `?` wildcards, which can be used to control the name of staged files. The following table shows how the wildcards are replaced depending on the arity of the received input collection.
+The target input file name may contain the `*` and `?` wildcards, which can be used to control the name of staged files. The following table shows how the wildcards are replaced depending on the cardinality of the received input collection.
 
-| Arity       | Name pattern | Staged file names                                                                                       |
+| Cardinality | Name pattern | Staged file names                                                                                       |
 | ----------- | ------------ | ------------------------------------------------------------------------------------------------------- |
 | any         | `*`          | named as the source file                                                                                |
 | 1           | `file*.ext`  | `file.ext`                                                                                              |
@@ -935,19 +937,19 @@ Available options:
 `arity`
 : :::{versionadded} 23.09.0-edge
   :::
-: Specify the number of expected files (default: ``'1..*'``, or ``'0..*'`` if the output is declared optional). Can be a number or a range:
+: Specify the number of expected files. Can be a number or a range:
 
   ```groovy
   output:
       path('one.txt', arity: '1')         // exactly one file is expected
       path('pair_*.txt', arity: '2')      // exactly two files are expected
       path('many_*.txt', arity: '1..*')   // one or more files are expected
-      path('optional.txt', arity: '0..1') // zero or one file is expected (equivalent to optional: true)
+      path('optional.txt', arity: '0..1') // zero or one file is expected
   ```
 
-  When a task completes, Nextflow will check whether the produced files for each path output match the declared arity, and fail if they do not.
+  When a task completes, Nextflow will check whether the produced files for each path output match the declared arity, and fail if they do not. If the arity is *single* (i.e. either `1` or `0..1`), a single file will be emitted. Otherwise, a list will always be emitted, even if only one file is produced.
 
-  If you declare an output as optional and also give it an arity, the optional flag will be ignored.
+  An output is *nullable* if the arity is exactly `0..1`. Whereas optional outputs emit nothing if the output file does not exist, nullable outputs emit a "null" file that can only be accepted by a nullable `path` input.
 
 `followLinks`
 : When `true` target files are return in place of any matching symlink (default: `true`)
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 12ef8d0cb0..f957607762 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1567,6 +1567,10 @@ 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.isNullable() ) {
+                    file = null
+                    exists = true
+                }
                 if( exists )
                     result = [file]
                 else
@@ -1584,10 +1588,10 @@ class TaskProcessor {
             }
         }
 
-        if( param.arity && !param.arity.contains(allFiles.size()) )
+        if( !param.isValidArity(allFiles.size()) )
             throw new IllegalArgumentException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
 
-        task.setOutput( param, allFiles.size()==1 && (!param.arity || param.arity.isSingle()) ? allFiles[0] : allFiles )
+        task.setOutput( param, allFiles.size()==1 && param.isSingle() ? allFiles[0] : allFiles )
 
     }
 
@@ -1789,7 +1793,7 @@ class TaskProcessor {
         if( obj instanceof Path )
             return obj
 
-        if( !obj == null )
+        if( obj == null )
             throw new ProcessUnrecoverableException("Path value cannot be null")
         
         if( !(obj instanceof CharSequence) )
@@ -1808,7 +1812,7 @@ class TaskProcessor {
         throw new ProcessUnrecoverableException("Not a valid path value: '$str'")
     }
 
-    protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch ) {
+    protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, boolean nullable, FilePorter.Batch batch ) {
 
         Collection allItems = obj instanceof Collection ? obj : [obj]
         def len = allItems.size()
@@ -1816,6 +1820,8 @@ class TaskProcessor {
         // use a bag so that cache hash key is not affected by file entries order
         def files = new ArrayBag<FileHolder>(len)
         for( def item : allItems ) {
+            if( item == null && nullable )
+                continue
 
             if( item instanceof Path || coerceToPath ) {
                 def path = normalizeToPath(item)
@@ -2031,23 +2037,21 @@ class TaskProcessor {
         for( Map.Entry<FileInParam,?> entry : secondPass.entrySet() ) {
             final param = entry.getKey()
             final val = entry.getValue()
-            final fileParam = param as FileInParam
-
-            def files = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
-            files = expandWildcards( fileParam.getFilePattern(ctx), files )
+            final normalized = normalizeInputToFiles(val, count, param.isPathQualifier(), param.isNullable(), batch)
+            final resolved = expandWildcards( param.getFilePattern(ctx), normalized )
 
-            if( param.arity && !param.arity.contains(files.size()) )
-                throw new IllegalArgumentException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${files.size()}")
+            if( !param.isValidArity(resolved.size()) )
+                throw new IllegalArgumentException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${resolved.size()}")
 
-            ctx.put( param.name, singleItemOrList(files, !param.arity || param.arity.isSingle(), task.type) )
-            count += files.size()
-            for( FileHolder item : files ) {
+            ctx.put( param.name, singleItemOrList(resolved, param.isSingle(), task.type) )
+            count += resolved.size()
+            for( FileHolder item : resolved ) {
                 Integer num = allNames.getOrCreate(item.stageName, 0) +1
                 allNames.put(item.stageName,num)
             }
 
             // add the value to the task instance context
-            task.setInput(param, files)
+            task.setInput(param, resolved)
         }
 
         // -- set the delegate map as context in the task config
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index f259934854..dc9045ee07 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -54,6 +54,24 @@ trait ArityParam {
         throw new IllegalArgumentException("Path arity should be a number (e.g. '1') or a range (e.g. '1..*')")
     }
 
+    /**
+     * Determine whether a null file is allowed.
+     */
+    boolean isNullable() {
+        return arity && arity.min == 0 && arity.max == 1
+    }
+
+    /**
+     * Determine whether a single output file should be unwrapped.
+     */
+    boolean isSingle() {
+        return !arity || arity.max == 1
+    }
+
+    boolean isValidArity(int size) {
+        return !arity || arity.contains(size)
+    }
+
     @EqualsAndHashCode
     static class Range {
         int min
@@ -68,10 +86,6 @@ trait ArityParam {
             min <= value && value <= max
         }
 
-        boolean isSingle() {
-            max == 1
-        }
-
         @Override
         String toString() {
             min == max
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
index 4104ba15f0..70cbca64fe 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
@@ -37,12 +37,15 @@ class ArityParamTest extends Specification {
         then:
         param.arity.min == MIN
         param.arity.max == MAX
+        param.isNullable() == NULLABLE
+        param.isSingle() == SINGLE
 
         where:
-        VALUE  | MIN | MAX
-        '1'    | 1   | 1
-        '0..1' | 0   | 1
-        '1..*' | 1   | Integer.MAX_VALUE
+        VALUE  | NULLABLE | SINGLE | MIN | MAX
+        '1'    | false    | true   | 1   | 1
+        '0..1' | true     | true   | 0   | 1
+        '1..*' | false    | false  | 1   | Integer.MAX_VALUE
+        '0..*' | false    | false  | 0   | Integer.MAX_VALUE
     }
 
     @Unroll
@@ -52,14 +55,13 @@ class ArityParamTest extends Specification {
         def range = new ArityParam.Range(MIN, MAX)
         then:
         range.contains(2) == TWO
-        range.isSingle() == SINGLE
         range.toString() == STRING
 
         where:
-        MIN | MAX               | TWO   | SINGLE | STRING
-        1   | 1                 | false | true   | '1'
-        0   | 1                 | false | true   | '0..1'
-        1   | Integer.MAX_VALUE | true  | false  | '1..*'
+        MIN | MAX               | TWO   | STRING
+        1   | 1                 | false | '1'
+        0   | 1                 | false | '0..1'
+        1   | Integer.MAX_VALUE | true  | '1..*'
     }
 
 }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
index 5ff28aac75..e479925314 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
+++ b/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) ?: SysEnv.get('NXF_AWS_SSE_MODE')
-        this.storageKmsKeyId = opts.storageKmsKeyId ?: SysEnv.get('NXF_AWS_SSE_KMS_KEY_ID')
+        this.storageEncryption = parseStorageEncryption(opts.storageEncryption as String)
+        this.storageKmsKeyId = opts.storageKmsKeyId
         this.pathStyleAccess = opts.s3PathStyleAccess as Boolean
         this.s3Acl = parseS3Acl(opts.s3Acl as String)
     }
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
index 0f5cd1f643..116a64456b 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
@@ -121,18 +121,4 @@ 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()
-    }
 }
diff --git a/tests/process-arity.nf b/tests/process-arity.nf
index 1fa121ce60..4ecfba109c 100644
--- a/tests/process-arity.nf
+++ b/tests/process-arity.nf
@@ -5,7 +5,7 @@ process foo {
     path('one.txt', arity: '1')
     path('pair_*.txt', arity: '2')
     path('many_*.txt', arity: '1..*')
-    path('optional.txt', arity: '0..1')
+    path('nullable.txt', arity: '0..1')
   script:
     """
     echo 'one' > one.txt
@@ -22,13 +22,13 @@ process bar {
     path('one.txt', arity: '1')
     path('pair_*.txt', arity: '2')
     path('many_*.txt', arity: '1..*')
-    path('optional.txt', arity: '0..1')
+    path('nullable.txt', arity: '0..1')
   script:
     """
     cat one.txt
     cat pair_*.txt
     cat many_*.txt
-    [[ -f optional.txt ]] && cat optional.txt || true
+    [[ -f nullable.txt ]] && cat nullable.txt || true
     """
 }
 

From 356a70d8905cad9feabcc644a28095be1a746031 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 16 Aug 2023 10:03:54 -0500
Subject: [PATCH 12/16] Add e2e test

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 tests/checks/process-arity-fails.nf/.checks | 18 ++++++++++++++++++
 tests/checks/process-arity.nf/.checks       | 16 ++++++++++++++++
 tests/process-arity-fails.nf                | 19 +++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 tests/checks/process-arity-fails.nf/.checks
 create mode 100644 tests/checks/process-arity.nf/.checks
 create mode 100644 tests/process-arity-fails.nf

diff --git a/tests/checks/process-arity-fails.nf/.checks b/tests/checks/process-arity-fails.nf/.checks
new file mode 100644
index 0000000000..346e4a2ea0
--- /dev/null
+++ b/tests/checks/process-arity-fails.nf/.checks
@@ -0,0 +1,18 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] && exit 1
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] && exit 1
+
+exit 0
\ No newline at end of file
diff --git a/tests/checks/process-arity.nf/.checks b/tests/checks/process-arity.nf/.checks
new file mode 100644
index 0000000000..66e9a3e265
--- /dev/null
+++ b/tests/checks/process-arity.nf/.checks
@@ -0,0 +1,16 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] || false
\ No newline at end of file
diff --git a/tests/process-arity-fails.nf b/tests/process-arity-fails.nf
new file mode 100644
index 0000000000..9f2c62cc01
--- /dev/null
+++ b/tests/process-arity-fails.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  output:
+    path('output.txt', arity: '0..1')
+  script:
+    true
+}
+
+process bar {
+  input:
+    path(file)
+  script:
+    true
+}
+
+workflow {
+    foo | bar
+}
\ No newline at end of file

From b63ec869ae6b701211f17b36cabe4f55fa1b8ffb Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 16 Aug 2023 10:04:56 -0500
Subject: [PATCH 13/16] Add NullPath

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy   | 15 +++----
 .../main/groovy/nextflow/util/NullPath.groovy | 41 +++++++++++++++++++
 2 files changed, 49 insertions(+), 7 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index f957607762..68425680ee 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -103,6 +103,7 @@ import nextflow.util.CacheHelper
 import nextflow.util.Escape
 import nextflow.util.LockManager
 import nextflow.util.LoggerHelper
+import nextflow.util.NullPath
 import nextflow.util.TestOnly
 import org.codehaus.groovy.control.CompilerConfiguration
 import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
@@ -1568,7 +1569,7 @@ class TaskProcessor {
                 def file = workDir.resolve(path)
                 def exists = param.followLinks ? file.exists() : file.exists(LinkOption.NOFOLLOW_LINKS)
                 if( !exists && param.isNullable() ) {
-                    file = null
+                    file = new NullPath(path)
                     exists = true
                 }
                 if( exists )
@@ -1789,11 +1790,14 @@ class TaskProcessor {
         return new FileHolder(source, result)
     }
 
-    protected Path normalizeToPath( obj ) {
+    protected Path normalizeToPath( obj, boolean nullable ) {
+        if( obj instanceof NullPath && !nullable )
+            throw new ProcessUnrecoverableException("Path value cannot be null")
+
         if( obj instanceof Path )
             return obj
 
-        if( obj == null )
+        if( !obj == null )
             throw new ProcessUnrecoverableException("Path value cannot be null")
         
         if( !(obj instanceof CharSequence) )
@@ -1820,11 +1824,8 @@ class TaskProcessor {
         // use a bag so that cache hash key is not affected by file entries order
         def files = new ArrayBag<FileHolder>(len)
         for( def item : allItems ) {
-            if( item == null && nullable )
-                continue
-
             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/util/NullPath.groovy b/modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy
new file mode 100644
index 0000000000..9ef1ab23c1
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/util/NullPath.groovy
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2013-2023, 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 java.nio.file.Paths
+
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.PackageScope
+import groovy.util.logging.Slf4j
+
+/**
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@EqualsAndHashCode
+@Slf4j
+class NullPath implements Path {
+
+    @PackageScope
+    @Delegate
+    Path delegate
+
+    NullPath(String path) {
+        delegate = Paths.get(path)
+    }
+}
\ No newline at end of file

From 76de19771f3e61880dfa122498710ef453b9b3b0 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 16 Aug 2023 10:25:57 -0500
Subject: [PATCH 14/16] Fail if nullable input receives a list

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy     | 11 ++++++++---
 .../nextflow/script/params/ArityParam.groovy    | 17 +++++++++++++++--
 tests/process-arity.nf                          |  4 ++--
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 68425680ee..3bc92aa5fd 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1589,7 +1589,7 @@ class TaskProcessor {
             }
         }
 
-        if( !param.isValidArity(allFiles.size()) )
+        if( !param.isValidArity(allFiles) )
             throw new IllegalArgumentException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
 
         task.setOutput( param, allFiles.size()==1 && param.isSingle() ? allFiles[0] : allFiles )
@@ -1824,6 +1824,7 @@ class TaskProcessor {
         // use a bag so that cache hash key is not affected by file entries order
         def files = new ArrayBag<FileHolder>(len)
         for( def item : allItems ) {
+
             if( item instanceof Path || coerceToPath ) {
                 def path = normalizeToPath(item, nullable)
                 def target = executor.isForeignFile(path) ? batch.addToForeign(path) : path
@@ -2041,8 +2042,12 @@ class TaskProcessor {
             final normalized = normalizeInputToFiles(val, count, param.isPathQualifier(), param.isNullable(), batch)
             final resolved = expandWildcards( param.getFilePattern(ctx), normalized )
 
-            if( !param.isValidArity(resolved.size()) )
-                throw new IllegalArgumentException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${resolved.size()}")
+            if( !param.isValidArity(resolved) ) {
+                final msg = param.isNullable()
+                    ? "expected a nullable file (0..1) but a list was provided"
+                    : "expected ${param.arity}, found ${resolved.size()}"
+                throw new IllegalArgumentException("Incorrect number of input files for process `${safeTaskName(task)}` -- ${msg}")
+            }
 
             ctx.put( param.name, singleItemOrList(resolved, param.isSingle(), task.type) )
             count += resolved.size()
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
index dc9045ee07..0b61faebc4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -68,8 +68,21 @@ trait ArityParam {
         return !arity || arity.max == 1
     }
 
-    boolean isValidArity(int size) {
-        return !arity || arity.contains(size)
+    /**
+     * Determine whether a collection of files has valid arity.
+     *
+     * If the param is nullable, there should be exactly one file (either
+     * a real file or a null file)
+     *
+     * @param files
+     */
+    boolean isValidArity(Collection files) {
+        if( !arity )
+            return true
+
+        return isNullable()
+            ? files.size() == 1
+            : arity.contains(files.size())
     }
 
     @EqualsAndHashCode
diff --git a/tests/process-arity.nf b/tests/process-arity.nf
index 4ecfba109c..9c2eca7030 100644
--- a/tests/process-arity.nf
+++ b/tests/process-arity.nf
@@ -22,13 +22,13 @@ process bar {
     path('one.txt', arity: '1')
     path('pair_*.txt', arity: '2')
     path('many_*.txt', arity: '1..*')
-    path('nullable.txt', arity: '0..1')
+    path(x, arity: '0..1')
   script:
     """
     cat one.txt
     cat pair_*.txt
     cat many_*.txt
-    [[ -f nullable.txt ]] && cat nullable.txt || true
+    [[ -f ${x} ]] && cat ${x} || true
     """
 }
 

From 4be12369e3320b7c42e042fd003842c9ead54422 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 16 Aug 2023 11:02:16 -0500
Subject: [PATCH 15/16] Add `arity: true` to infer arity from file pattern

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md                                        |  6 +++++-
 .../groovy/nextflow/script/params/FileInParam.groovy   | 10 ++++++++++
 .../groovy/nextflow/script/params/FileOutParam.groovy  | 10 ++++++++++
 .../groovy/nextflow/script/params/ParamsInTest.groovy  |  9 ++++++---
 4 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/docs/process.md b/docs/process.md
index cfd6a3d317..592ce14064 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -490,6 +490,8 @@ Available options:
 
   An input is *nullable* if the arity is exactly `0..1`. Nullable inputs can accept "null" files from nullable `path` outputs.
 
+  You can also set `arity: true` to infer the arity from the file pattern: `1..*` if the pattern is a glob, `1` otherwise.
+
 `stageAs`
 : Specify how the file should be named in the task work directory:
 
@@ -508,7 +510,7 @@ Available options:
   }
   ```
 
-  Cab be a name or a pattern as described in the [Multiple input files](#multiple-input-files) section.
+  Can be a name or a pattern as described in the [Multiple input files](#multiple-input-files) section.
 
 ### Multiple input files
 
@@ -951,6 +953,8 @@ Available options:
 
   An output is *nullable* if the arity is exactly `0..1`. Whereas optional outputs emit nothing if the output file does not exist, nullable outputs emit a "null" file that can only be accepted by a nullable `path` input.
 
+  You can also set `arity: true` to infer the arity from the file pattern: `1..*` if the pattern is a glob, `1` otherwise.
+
 `followLinks`
 : When `true` target files are return in place of any matching symlink (default: `true`)
 
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 8bebf83d70..ae0ac4da5f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -153,4 +153,14 @@ class FileInParam extends BaseInParam implements ArityParam, PathQualifier {
         return this
     }
 
+    def setArity(boolean value) {
+        if( !value )
+            return
+
+        final str = filePattern?.contains('*') || filePattern?.contains('?')
+            ? '1..*'
+            : '1'
+        setArity(str)
+    }
+
 }
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 a55cd957c7..085e662449 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -276,4 +276,14 @@ class FileOutParam extends BaseOutParam implements OutParam, ArityParam, Optiona
         (FileOutParam)super.setOptions(opts)
     }
 
+    def setArity(boolean value) {
+        if( !value )
+            return
+
+        final str = filePattern?.contains('*') || filePattern?.contains('?')
+            ? '1..*'
+            : '1'
+        setArity(str)
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
index 3312a37a3c..8f8a033a92 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
@@ -710,9 +710,9 @@ class ParamsInTest extends Dsl2Spec {
               path x, arity: '1'
               path f1, arity: '1..2'
               path '*.fa', arity: '1..*'
-              path 'file.txt'
-              path f2, name: '*.fa'
-              path f3, stageAs: '*.txt'
+              path 'file.txt', arity: true
+              path f2, name: '*.fa', arity: true
+              path f3, stageAs: '*.txt', arity: true
 
               return ''
             }
@@ -759,16 +759,19 @@ class ParamsInTest extends Dsl2Spec {
         in3.inChannel.val == FILE
         in3.index == 3
         in3.isPathQualifier()
+        in3.arity == new ArityParam.Range(1, 1)
 
         in4.name == 'f2'
         in4.filePattern == '*.fa'
         in4.index == 4
         in4.isPathQualifier()
+        in4.arity == new ArityParam.Range(1, Integer.MAX_VALUE)
 
         in5.name == 'f3'
         in5.filePattern == '*.txt'
         in5.index == 5
         in5.isPathQualifier()
+        in5.arity == new ArityParam.Range(1, Integer.MAX_VALUE)
     }
 
     def 'test input paths with gstring'() {

From b6a5fb37066baf722a0d38a1461b03830338c1fe Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 16 Aug 2023 11:10:37 -0500
Subject: [PATCH 16/16] Fix failing tests

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/processor/TaskProcessor.groovy     | 2 +-
 .../src/test/groovy/nextflow/processor/TaskProcessorTest.groovy | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 3bc92aa5fd..8c468898e4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1790,7 +1790,7 @@ class TaskProcessor {
         return new FileHolder(source, result)
     }
 
-    protected Path normalizeToPath( obj, boolean nullable ) {
+    protected Path normalizeToPath( obj, boolean nullable=false ) {
         if( obj instanceof NullPath && !nullable )
             throw new ProcessUnrecoverableException("Path value cannot be null")
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index 471699f812..71bafeb50d 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -829,7 +829,7 @@ class TaskProcessorTest extends Specification {
         def proc = new TaskProcessor(); proc.executor = executor
 
         when:
-        def result = proc.normalizeInputToFiles(PATH.toString(), 0, true, batch)
+        def result = proc.normalizeInputToFiles(PATH.toString(), 0, true, false, batch)
         then:
         1 * executor.isForeignFile(PATH) >> false
         0 * batch.addToForeign(PATH) >> null