nextflow-io · bentsherman · Jan 7, 2026 · Jan 2, 2026 · Jan 2, 2026 · Jan 6, 2026
@@ -112,6 +112,12 @@ The following settings are available:
 `aws.batch.executionRole`
 : The AWS Batch [Execution Role](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) ARN that needs to be used to execute the Batch Job. It is mandatory when using AWS Fargate.
 
+`aws.batch.forceGlacierTransfer`
+: :::{versionadded 26.04.0}
+  :::
+: When `true`, add the `--force-glacier-transfer` flag to AWS CLI S3 download commands (default: `false`).
+: This option is needed when staging directories that have been restored from [S3 Glacier](https://aws.amazon.com/s3/storage-classes/glacier/). It does not restore objects from Glacier.
+
 `aws.batch.jobRole`
 : The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
 

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy
@@ -164,4 +164,8 @@ class AwsOptions implements CloudTransferOptions {
         return awsConfig.batchConfig.terminateUnschedulableJobs
     }
 
+    Boolean getForceGlacierTransfer() {
+        return awsConfig.batchConfig.forceGlacierTransfer
+    }
+
 }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
@@ -59,6 +59,12 @@ class AwsBatchConfig implements CloudTransferOptions, ConfigScope {
     """)
     final String executionRole
 
+    @ConfigOption
+    @Description("""
+        When `true`, add the `--force-glacier-transfer` flag to AWS CLI S3 download commands (default: `false`).
+    """)
+    final boolean forceGlacierTransfer
+
     @ConfigOption
     @Description("""
         The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
@@ -151,6 +157,7 @@ class AwsBatchConfig implements CloudTransferOptions, ConfigScope {
         schedulingPriority = opts.schedulingPriority as Integer ?: 0
         executionRole = opts.executionRole
         terminateUnschedulableJobs = opts.terminateUnschedulableJobs as boolean
+        forceGlacierTransfer = opts.forceGlacierTransfer as boolean
         if( retryMode == 'built-in' )
             retryMode = null // this force falling back on NF built-in retry mode instead of delegating to AWS CLI tool
         if( retryMode && retryMode !in AwsOptions.VALID_RETRY_MODES )

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
@@ -38,6 +38,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
     private String s5cmdPath
     private String acl = ''
     private String requesterPays = ''
+    private String forceGlacierTransfer = ''
 
     S3BashLib withCliPath(String cliPath) {
         if( cliPath )
@@ -90,12 +91,17 @@ class S3BashLib extends BashFunLib<S3BashLib> {
         return this
     }
 
+    S3BashLib withForceGlacierTransfer(Boolean value) {
+        this.forceGlacierTransfer = value ? '--force-glacier-transfer ' : ''
+        return this
+    }
+
     protected String retryEnv() {
         if( !retryMode )
             return ''
         """
         # aws cli retry config
-        export AWS_RETRY_MODE=${retryMode} 
+        export AWS_RETRY_MODE=${retryMode}
         export AWS_MAX_ATTEMPTS=${maxTransferAttempts}
         """.stripIndent().rightTrim()
     }
@@ -126,8 +132,8 @@ class S3BashLib extends BashFunLib<S3BashLib> {
             local file_name=\$(basename \$1)
             local is_dir=\$($cli s3 ls \$source | grep -F "PRE \${file_name}/" -c)
             if [[ \$is_dir == 1 ]]; then
-                $cli s3 cp --only-show-errors --recursive "\$source" "\$target"
-            else 
+                $cli s3 cp --only-show-errors --recursive ${forceGlacierTransfer}"\$source" "\$target"
+            else
                 $cli s3 cp --only-show-errors "\$source" "\$target"
             fi
         }
@@ -165,7 +171,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
             local is_dir=\$($cli ls \$source | grep -F "DIR  \${file_name}/" -c)
             if [[ \$is_dir == 1 ]]; then
                 $cli cp "\$source/*" "\$target"
-            else 
+            else
                 $cli cp "\$source" "\$target"
             fi
         }
@@ -194,6 +200,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
                 .withS5cmdPath( opts.s5cmdPath )
                 .withAcl( opts.s3Acl )
                 .withRequesterPays( opts.requesterPays )
+                .withForceGlacierTransfer( opts.forceGlacierTransfer )
     }
 
     static String script(AwsOptions opts) {

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
@@ -205,7 +205,7 @@ class AwsBatchFileCopyStrategyTest extends Specification {
                         local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                         if [[ $is_dir == 1 ]]; then
                             aws s3 cp --only-show-errors --recursive "$source" "$target"
-                        else 
+                        else
                             aws s3 cp --only-show-errors "$source" "$target"
                         fi
                     }
@@ -296,7 +296,7 @@ class AwsBatchFileCopyStrategyTest extends Specification {
                     local is_dir=$(/foo/aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                     if [[ $is_dir == 1 ]]; then
                         /foo/aws s3 cp --only-show-errors --recursive "$source" "$target"
-                    else 
+                    else
                         /foo/aws s3 cp --only-show-errors "$source" "$target"
                     fi
                 }

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
@@ -139,7 +139,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                     local is_dir=$(/conda/bin/aws --region eu-west-1 s3 ls $source | grep -F "PRE ${file_name}/" -c)
                     if [[ $is_dir == 1 ]]; then
                         /conda/bin/aws --region eu-west-1 s3 cp --only-show-errors --recursive "$source" "$target"
-                    else 
+                    else
                         /conda/bin/aws --region eu-west-1 s3 cp --only-show-errors "$source" "$target"
                     fi
                 }
@@ -318,7 +318,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                         local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                         if [[ $is_dir == 1 ]]; then
                             aws s3 cp --only-show-errors --recursive "$source" "$target"
-                        else 
+                        else
                             aws s3 cp --only-show-errors "$source" "$target"
                         fi
                     }
@@ -490,7 +490,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                         local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                         if [[ $is_dir == 1 ]]; then
                             aws s3 cp --only-show-errors --recursive "$source" "$target"
-                        else 
+                        else
                             aws s3 cp --only-show-errors "$source" "$target"
                         fi
                     }
@@ -584,7 +584,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                     }
 
                     # aws cli retry config
-                    export AWS_RETRY_MODE=adaptive 
+                    export AWS_RETRY_MODE=adaptive
                     export AWS_MAX_ATTEMPTS=3
                     # aws helper
                     nxf_s3_upload() {
@@ -606,7 +606,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                         local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                         if [[ $is_dir == 1 ]]; then
                             aws s3 cp --only-show-errors --recursive "$source" "$target"
-                        else 
+                        else
                             aws s3 cp --only-show-errors "$source" "$target"
                         fi
                     }

diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy
@@ -47,6 +47,7 @@ class AwsBatchConfigTest extends Specification {
         !batch.s5cmdPath
         batch.schedulingPriority == 0
         !batch.terminateUnschedulableJobs
+        !batch.forceGlacierTransfer
     }
 
     def 'should create config with options' () {
@@ -153,4 +154,18 @@ class AwsBatchConfigTest extends Specification {
         [terminateUnschedulableJobs: false]     | false
         [terminateUnschedulableJobs: true]      | true
     }
+
+    def 'should parse forceGlacierTransfer flag' () {
+        given:
+        def opts = new AwsBatchConfig(OPTS)
+
+        expect:
+        opts.forceGlacierTransfer == FORCE_GLACIER
+
+        where:
+        OPTS                                    | FORCE_GLACIER
+        [:]                                     | false
+        [forceGlacierTransfer: false]           | false
+        [forceGlacierTransfer: true]            | true
+    }
 }
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
@@ -104,7 +104,7 @@ class S3BashLibTest extends Specification {
                         local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                         if [[ $is_dir == 1 ]]; then
                             aws s3 cp --only-show-errors --recursive "$source" "$target"
-                        else 
+                        else
                             aws s3 cp --only-show-errors "$source" "$target"
                         fi
                     }
@@ -203,7 +203,7 @@ class S3BashLibTest extends Specification {
                         local is_dir=$(/foo/bin/aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                         if [[ $is_dir == 1 ]]; then
                             /foo/bin/aws s3 cp --only-show-errors --recursive "$source" "$target"
-                        else 
+                        else
                             /foo/bin/aws s3 cp --only-show-errors "$source" "$target"
                         fi
                     }
@@ -223,7 +223,7 @@ class S3BashLibTest extends Specification {
         expect:
         S3BashLib.script()  == '''
             # aws cli retry config
-            export AWS_RETRY_MODE=standard 
+            export AWS_RETRY_MODE=standard
             export AWS_MAX_ATTEMPTS=5
             # aws helper
             nxf_s3_upload() {
@@ -245,7 +245,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -261,7 +261,7 @@ class S3BashLibTest extends Specification {
         expect:
         S3BashLib.script()  == '''
             # aws cli retry config
-            export AWS_RETRY_MODE=legacy 
+            export AWS_RETRY_MODE=legacy
             export AWS_MAX_ATTEMPTS=100
             # aws helper
             nxf_s3_upload() {
@@ -283,7 +283,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -318,7 +318,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -334,7 +334,7 @@ class S3BashLibTest extends Specification {
         expect:
         S3BashLib.script() == '''
             # aws cli retry config
-            export AWS_RETRY_MODE=legacy 
+            export AWS_RETRY_MODE=legacy
             export AWS_MAX_ATTEMPTS=99
             # aws helper
             nxf_s3_upload() {
@@ -356,7 +356,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(/some/bin/aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     /some/bin/aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     /some/bin/aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -450,7 +450,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -541,7 +541,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -616,7 +616,7 @@ class S3BashLibTest extends Specification {
             }
 
             # aws cli retry config
-            export AWS_RETRY_MODE=standard 
+            export AWS_RETRY_MODE=standard
             export AWS_MAX_ATTEMPTS=5
             # aws helper
             nxf_s3_upload() {
@@ -638,7 +638,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -714,7 +714,7 @@ class S3BashLibTest extends Specification {
             }
 
             # aws cli retry config
-            export AWS_RETRY_MODE=standard 
+            export AWS_RETRY_MODE=standard
             export AWS_MAX_ATTEMPTS=5
             # aws helper
             nxf_s3_upload() {
@@ -736,7 +736,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     aws s3 cp --only-show-errors --recursive "$source" "$target"
-                else 
+                else
                     aws s3 cp --only-show-errors "$source" "$target"
                 fi
             }
@@ -773,7 +773,7 @@ class S3BashLibTest extends Specification {
                 local is_dir=$(s5cmd ls $source | grep -F "DIR  ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     s5cmd cp "$source/*" "$target"
-                else 
+                else
                     s5cmd cp "$source" "$target"
                 fi
             }
@@ -802,20 +802,58 @@ class S3BashLibTest extends Specification {
                   s5cmd cp --acl public-read --storage-class STANDARD "$name" "$s3path/$name"
                 fi
             }
-            
+
             nxf_s3_download() {
                 local source=$1
                 local target=$2
                 local file_name=$(basename $1)
                 local is_dir=$(s5cmd ls $source | grep -F "DIR  ${file_name}/" -c)
                 if [[ $is_dir == 1 ]]; then
                     s5cmd cp "$source/*" "$target"
-                else 
+                else
                     s5cmd cp "$source" "$target"
                 fi
             }
             '''.stripIndent(true)
     }
-
+
+    def 'should create script with force glacier transfer' () {
+        given:
+        Global.session = Mock(Session) {
+            getConfig() >> [aws:[batch:[forceGlacierTransfer: true]]]
+        }
+
+        expect:
+        S3BashLib.script()  == '''
+            # aws cli retry config
+            export AWS_RETRY_MODE=standard
+            export AWS_MAX_ATTEMPTS=5
+            # aws helper
+            nxf_s3_upload() {
+                local name=$1
+                local s3path=$2
+                if [[ "$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"
+                fi
+            }
+
+            nxf_s3_download() {
+                local source=$1
+                local target=$2
+                local file_name=$(basename $1)
+                local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
+                if [[ $is_dir == 1 ]]; then
+                    aws s3 cp --only-show-errors --recursive --force-glacier-transfer "$source" "$target"
+                else
+                    aws s3 cp --only-show-errors "$source" "$target"
+                fi
+            }
+            '''.stripIndent(true)
+    }
+
 
 }