diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy
index 25ab24a205..d79ec957e3 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy
@@ -134,8 +134,7 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      */
     @Override
     String touchFile( Path file ) {
-        final aws = opts.getAwsCli()
-        "echo start | $aws s3 cp --only-show-errors - s3:/${Escape.path(file)}"
+        "echo start | nxf_s3_upload - s3:/${Escape.path(file)}"
     }
 
     /**
@@ -162,8 +161,7 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      * {@inheritDoc}
      */
     String exitFile( Path path ) {
-        final aws = opts.getAwsCli()
-        "| $aws s3 cp --only-show-errors - s3:/${Escape.path(path)} || true"
+        "| nxf_s3_upload - s3:/${Escape.path(path)} || true"
     }
 
     /**
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
index ad549ce2da..8f075178de 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
@@ -28,7 +28,7 @@ import nextflow.executor.BashFunLib
 class S3BashLib extends BashFunLib<S3BashLib> {
 
     private String storageClass = 'STANDARD'
-    private String encryptionEncryption = ''
+    private String storageEncryption = ''
     private String debug = ''
     private String cli = 'aws'
     private String retryMode
@@ -58,7 +58,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
 
     S3BashLib withStorageEncryption(String value) {
         if( value )
-            this.encryptionEncryption = value ? "--sse $value " : ''
+            this.storageEncryption = value ? "--sse $value " : ''
         return this
     }
 
@@ -78,10 +78,12 @@ class S3BashLib extends BashFunLib<S3BashLib> {
         nxf_s3_upload() {
             local name=\$1
             local s3path=\$2
-            if [[ -d "\$name" ]]; then
-              $cli s3 cp --only-show-errors --recursive $debug$encryptionEncryption--storage-class $storageClass "\$name" "\$s3path/\$name"
+            if [[ "\$name" == - ]]; then
+              $cli s3 cp --only-show-errors $debug$storageEncryption--storage-class $storageClass - "\$s3path"
+            elif [[ -d "\$name" ]]; then
+              $cli s3 cp --only-show-errors --recursive $debug$storageEncryption--storage-class $storageClass "\$name" "\$s3path/\$name"
             else
-              $cli s3 cp --only-show-errors $debug$encryptionEncryption--storage-class $storageClass "\$name" "\$s3path/\$name"
+              $cli s3 cp --only-show-errors $debug$storageEncryption--storage-class $storageClass "\$name" "\$s3path/\$name"
             fi
         }
         
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy
index 047baefeeb..545bf64a2d 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy
@@ -33,9 +33,9 @@ class AwsBatchFileCopyStrategyTest extends Specification {
         def RUN = Paths.get('/some/data/.command.run')
         def copy = new AwsBatchFileCopyStrategy(Mock(TaskBean), new AwsOptions())
         expect:
-        copy.touchFile(RUN) == "echo start | aws s3 cp --only-show-errors - s3://some/data/.command.run"
+        copy.touchFile(RUN) == "echo start | nxf_s3_upload - s3://some/data/.command.run"
         copy.copyFile("nobel_prize_results.gz",Paths.get("/some/data/nobel_prize_results.gz")) == "nxf_s3_upload nobel_prize_results.gz s3://some/data"
-        copy.exitFile(EXIT) == "| aws s3 cp --only-show-errors - s3://some/path/.exitcode || true"
+        copy.exitFile(EXIT) == "| nxf_s3_upload - s3://some/path/.exitcode || true"
         copy.stageInputFile(FILE, 'foo.txt') == """
                                     downloads+=("nxf_s3_download s3://some/data/nobel_prize_results.gz foo.txt")
                                     """
@@ -188,7 +188,9 @@ class AwsBatchFileCopyStrategyTest extends Specification {
                     nxf_s3_upload() {
                         local name=$1
                         local s3path=$2
-                        if [[ -d "$name" ]]; then
+                        if [[ "$name" == - ]]; then
+                          aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                        elif [[ -d "$name" ]]; then
                           aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                         else
                           aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -275,7 +277,9 @@ class AwsBatchFileCopyStrategyTest extends Specification {
                 nxf_s3_upload() {
                     local name=$1
                     local s3path=$2
-                    if [[ -d "$name" ]]; then
+                    if [[ "$name" == - ]]; then
+                      /foo/aws s3 cp --only-show-errors --sse AES256 --storage-class STANDARD_IA - "$s3path"
+                    elif [[ -d "$name" ]]; then
                       /foo/aws s3 cp --only-show-errors --recursive --sse AES256 --storage-class STANDARD_IA "$name" "$s3path/$name"
                     else
                       /foo/aws s3 cp --only-show-errors --sse AES256 --storage-class STANDARD_IA "$name" "$s3path/$name"
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
index 00658ac8b7..7b06de8d2a 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -117,7 +117,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                 nxf_s3_upload() {
                     local name=$1
                     local s3path=$2
-                    if [[ -d "$name" ]]; then
+                    if [[ "$name" == - ]]; then
+                      /conda/bin/aws --region eu-west-1 s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                    elif [[ -d "$name" ]]; then
                       /conda/bin/aws --region eu-west-1 s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                     else
                       /conda/bin/aws --region eu-west-1 s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -292,7 +294,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                     nxf_s3_upload() {
                         local name=$1
                         local s3path=$2
-                        if [[ -d "$name" ]]; then
+                        if [[ "$name" == - ]]; then
+                          aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                        elif [[ -d "$name" ]]; then
                           aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                         else
                           aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -433,7 +437,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                     nxf_s3_upload() {
                         local name=$1
                         local s3path=$2
-                        if [[ -d "$name" ]]; then
+                        if [[ "$name" == - ]]; then
+                          aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                        elif [[ -d "$name" ]]; then
                           aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                         else
                           aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -548,7 +554,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                     nxf_s3_upload() {
                         local name=$1
                         local s3path=$2
-                        if [[ -d "$name" ]]; then
+                        if [[ "$name" == - ]]; then
+                          aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                        elif [[ -d "$name" ]]; then
                           aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                         else
                           aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
index 25cec34f8c..20058a7f7b 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
@@ -86,7 +86,9 @@ class S3BashLibTest extends Specification {
                     nxf_s3_upload() {
                         local name=$1
                         local s3path=$2
-                        if [[ -d "$name" ]]; then
+                        if [[ "$name" == - ]]; then
+                          aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                        elif [[ -d "$name" ]]; then
                           aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                         else
                           aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -181,7 +183,9 @@ class S3BashLibTest extends Specification {
                     nxf_s3_upload() {
                         local name=$1
                         local s3path=$2
-                        if [[ -d "$name" ]]; then
+                        if [[ "$name" == - ]]; then
+                          /foo/bin/aws s3 cp --only-show-errors --sse S-ENCRYPT --storage-class S-CLAZZ - "$s3path"
+                        elif [[ -d "$name" ]]; then
                           /foo/bin/aws s3 cp --only-show-errors --recursive --sse S-ENCRYPT --storage-class S-CLAZZ "$name" "$s3path/$name"
                         else
                           /foo/bin/aws s3 cp --only-show-errors --sse S-ENCRYPT --storage-class S-CLAZZ "$name" "$s3path/$name"
@@ -221,7 +225,9 @@ class S3BashLibTest extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -257,7 +263,9 @@ class S3BashLibTest extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -290,7 +298,9 @@ class S3BashLibTest extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -326,7 +336,9 @@ class S3BashLibTest extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  /some/bin/aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   /some/bin/aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   /some/bin/aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -416,7 +428,9 @@ class S3BashLibTest extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -503,7 +517,9 @@ class S3BashLibTest extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
diff --git a/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy b/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
index e4609ac45d..b2089d9d0b 100644
--- a/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
@@ -72,7 +72,9 @@ class BashWrapperBuilderWithS3Test extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
@@ -188,7 +190,9 @@ class BashWrapperBuilderWithS3Test extends Specification {
             nxf_s3_upload() {
                 local name=$1
                 local s3path=$2
-                if [[ -d "$name" ]]; then
+                if [[ "$name" == - ]]; then
+                  aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
+                elif [[ -d "$name" ]]; then
                   aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
                 else
                   aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"