From dee69a8e44bea1aa466556cc71ab3af0d3b7acea Mon Sep 17 00:00:00 2001
From: Tomiles <116039+tomiles@users.noreply.github.com>
Date: Thu, 2 Apr 2026 22:49:57 +0200
Subject: [PATCH 1/6] feat(nf-google): add google.batch stage-in/out copy
 transports (posix, gcloud, gsutil)

Signed-off-by: Tomiles <116039+tomiles@users.noreply.github.com>
---
 .../google/batch/GoogleBatchBashLib.groovy    | 269 ++++++++++++++++++
 .../batch/GoogleBatchFileCopyStrategy.groovy  | 170 +++++++++++
 .../batch/GoogleBatchScriptLauncher.groovy    |  15 +-
 .../batch/GoogleBatchTaskHandler.groovy       |   2 +-
 .../google/batch/client/BatchConfig.groovy    |  92 ++++++
 .../GoogleBatchFileCopyStrategyTest.groovy    | 127 +++++++++
 .../batch/client/BatchConfigTest.groovy       |  41 ++-
 7 files changed, 711 insertions(+), 5 deletions(-)
 create mode 100644 plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy
 create mode 100644 plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
 create mode 100644 plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy
new file mode 100644
index 0000000000..619998a082
--- /dev/null
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy
@@ -0,0 +1,269 @@
+/*
+ * Copyright 2013-2026, 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.cloud.google.batch
+
+import groovy.transform.CompileStatic
+import groovy.transform.Memoized
+import nextflow.cloud.google.batch.client.BatchConfig
+import nextflow.executor.BashFunLib
+import nextflow.util.Escape
+
+/**
+ * Bash helpers for Google Cloud Storage transfers in Google Batch tasks.
+ * Order within each transport is controlled by {@code NXF_STAGE_IN_COPY_TRANSPORT} / {@code NXF_STAGE_OUT_COPY_TRANSPORT}.
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class GoogleBatchBashLib extends BashFunLib<GoogleBatchBashLib> {
+
+    private String gcloudCli = 'gcloud'
+
+    private String gsutilCli = 'gsutil'
+
+    private BatchConfig batchConfig
+
+    GoogleBatchBashLib withGcloudCli(String value) {
+        if( value )
+            this.gcloudCli = value
+        return this
+    }
+
+    GoogleBatchBashLib withGsutilCli(String value) {
+        if( value )
+            this.gsutilCli = value
+        return this
+    }
+
+    GoogleBatchBashLib withBatchConfig(BatchConfig config) {
+        this.batchConfig = config
+        return this
+    }
+
+    protected String gsLib() {
+        final gcloud = Escape.path(gcloudCli ?: 'gcloud')
+        final gsutil = Escape.path(gsutilCli ?: 'gsutil')
+        final mountRoot = GoogleBatchScriptLauncher.MOUNT_ROOT
+        """
+        export NXF_GCLOUD=$gcloud
+        export NXF_GSUTIL=$gsutil
+        export NXF_GS_MOUNT_ROOT="$mountRoot"
+
+        nxf_gs_uri_to_mount() {
+            case "\$1" in
+            gs://*)
+                local p=\${1#gs://}
+                local bucket=\${p%%/*}
+                if [[ "\$bucket" == "\$p" ]]; then
+                    echo "\$NXF_GS_MOUNT_ROOT/\$bucket"
+                else
+                    local rest=\${p#*/}
+                    echo "\$NXF_GS_MOUNT_ROOT/\$bucket/\$rest"
+                fi
+                ;;
+            *)
+                echo ""
+                ;;
+            esac
+        }
+
+        nxf_gs_download_gcloud() {
+            command -v "\$NXF_GCLOUD" >/dev/null 2>&1 || return 1
+            local source=\$1
+            local target=\$2
+            local basedir=\$(dirname "\$2")
+            mkdir -p "\$basedir"
+            if \$NXF_GCLOUD storage cp "\$source" "\$target" 2>/dev/null; then
+                return 0
+            fi
+            mkdir -p "\$target"
+            if \$NXF_GCLOUD storage cp --recursive "\$source" "\$target" >/dev/null 2>&1; then
+                return 0
+            fi
+            rm -rf "\$target"
+            return 1
+        }
+
+        nxf_gs_download_gsutil() {
+            command -v "\$NXF_GSUTIL" >/dev/null 2>&1 || return 1
+            local source=\$1
+            local target=\$2
+            local basedir=\$(dirname "\$2")
+            mkdir -p "\$basedir"
+            local ret
+            ret=\$(\$NXF_GSUTIL cp "\$source" "\$target" 2>&1) || {
+                mkdir -p "\$target"
+                \$NXF_GSUTIL -m cp -r "\$source" "\$target" >/dev/null || {
+                    rm -rf "\$target"
+                    return 1
+                }
+            }
+            return 0
+        }
+
+        nxf_gs_download_mount() {
+            local source=\$1
+            local target=\$2
+            local ms
+            ms=\$(nxf_gs_uri_to_mount "\$source")
+            [[ -n "\$ms" ]] || return 1
+            [[ -e "\$ms" || -d "\$ms" ]] || return 1
+            mkdir -p "\$(dirname "\$target")"
+            cp -fRL "\$ms" "\$target"
+        }
+
+        nxf_gs_download() {
+            local source=\$1
+            local target=\$2
+            case "\${NXF_STAGE_IN_COPY_TRANSPORT:-posix}" in
+            gsutil)
+                if nxf_gs_download_gsutil "\$source" "\$target"; then return 0; fi
+                if nxf_gs_download_gcloud "\$source" "\$target"; then return 0; fi
+                if nxf_gs_download_mount "\$source" "\$target"; then return 0; fi
+                ;;
+            gcloud)
+                if nxf_gs_download_gcloud "\$source" "\$target"; then return 0; fi
+                if nxf_gs_download_gsutil "\$source" "\$target"; then return 0; fi
+                if nxf_gs_download_mount "\$source" "\$target"; then return 0; fi
+                ;;
+            posix|*)
+                if nxf_gs_download_mount "\$source" "\$target"; then return 0; fi
+                ;;
+            esac
+            >&2 echo "Unable to download path: \$source"
+            exit 1
+        }
+
+        nxf_gs_upload_try_gcloud() {
+            command -v "\$NXF_GCLOUD" >/dev/null 2>&1 || return 1
+            local name=\$1
+            local gspath=\$2
+            if [[ "\$name" == '-' ]]; then
+                return 1
+            fi
+            if [[ -d "\$name" ]]; then
+                \$NXF_GCLOUD storage cp --recursive "\$name" "\$gspath/\$name"
+            else
+                \$NXF_GCLOUD storage cp "\$name" "\$gspath/\$name"
+            fi
+        }
+
+        nxf_gs_upload_try_gsutil() {
+            command -v "\$NXF_GSUTIL" >/dev/null 2>&1 || return 1
+            local name=\$1
+            local gspath=\$2
+            if [[ "\$name" == '-' ]]; then
+                return 1
+            fi
+            if [[ -d "\$name" ]]; then
+                \$NXF_GSUTIL -m cp -r "\$name" "\$gspath/\$name"
+            else
+                \$NXF_GSUTIL cp "\$name" "\$gspath/\$name"
+            fi
+        }
+
+        nxf_gs_upload_try_mount() {
+            local name=\$1
+            local gspath=\$2
+            if [[ "\$name" == '-' ]]; then
+                return 1
+            fi
+            local dest
+            dest=\$(nxf_gs_uri_to_mount "\$gspath/\$name")
+            [[ -n "\$dest" ]] || return 1
+            mkdir -p "\$(dirname "\$dest")"
+            cp -fRL "\$name" "\$dest"
+        }
+
+        nxf_gs_upload() {
+            local name=\$1
+            local gspath=\${2%/}
+            local move=\${3:-0}
+            if [[ "\$name" == '-' ]]; then
+                if command -v "\$NXF_GCLOUD" >/dev/null 2>&1 && \$NXF_GCLOUD storage cp - "\$gspath"; then
+                    :
+                elif command -v "\$NXF_GSUTIL" >/dev/null 2>&1 && \$NXF_GSUTIL cp - "\$gspath"; then
+                    :
+                else
+                    return 1
+                fi
+            else
+                case "\${NXF_STAGE_OUT_COPY_TRANSPORT:-posix}" in
+                gsutil)
+                    if nxf_gs_upload_try_gsutil "\$name" "\$gspath"; then :;
+                    elif nxf_gs_upload_try_gcloud "\$name" "\$gspath"; then :;
+                    elif nxf_gs_upload_try_mount "\$name" "\$gspath"; then :;
+                    else
+                        >&2 echo "Unable to upload path: \$name"
+                        return 1
+                    fi
+                    ;;
+                gcloud)
+                    if nxf_gs_upload_try_gcloud "\$name" "\$gspath"; then :;
+                    elif nxf_gs_upload_try_gsutil "\$name" "\$gspath"; then :;
+                    elif nxf_gs_upload_try_mount "\$name" "\$gspath"; then :;
+                    else
+                        >&2 echo "Unable to upload path: \$name"
+                        return 1
+                    fi
+                    ;;
+                posix|*)
+                    if nxf_gs_upload_try_mount "\$name" "\$gspath"; then :;
+                    else
+                        >&2 echo "Unable to upload path: \$name"
+                        return 1
+                    fi
+                    ;;
+                esac
+            fi
+            if [[ "\$move" == "1" && "\$name" != '-' ]]; then
+                rm -rf "\$name"
+            fi
+        }
+        """.stripIndent(true)
+    }
+
+    protected String transportExports() {
+        final cfg = batchConfig
+        if( !cfg )
+            return ''
+        final inTr = cfg.stageInCopyTransport ?: BatchConfig.COPY_TRANSPORT_POSIX
+        final outTr = cfg.stageOutCopyTransport ?: BatchConfig.COPY_TRANSPORT_POSIX
+        """
+        export NXF_STAGE_IN_COPY_TRANSPORT=${Escape.path(inTr)}
+        export NXF_STAGE_OUT_COPY_TRANSPORT=${Escape.path(outTr)}
+        """.stripIndent(true)
+    }
+
+    @Override
+    String render() {
+        super.render() + transportExports() + gsLib()
+    }
+
+    @Memoized
+    static String script(BatchConfig config) {
+        new GoogleBatchBashLib()
+                .includeCoreFun(true)
+                .withMaxParallelTransfers(config.maxParallelTransfers)
+                .withMaxTransferAttempts(config.maxTransferAttempts)
+                .withDelayBetweenAttempts(config.delayBetweenAttempts)
+                .withGcloudCli(config.gcloudCli)
+                .withGsutilCli(config.gsutilCli)
+                .withBatchConfig(config)
+                .render()
+    }
+}
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
new file mode 100644
index 0000000000..891355d44a
--- /dev/null
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
@@ -0,0 +1,170 @@
+/*
+ * Copyright 2013-2026, 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.cloud.google.batch
+
+import java.nio.file.Path
+
+import com.google.cloud.storage.contrib.nio.CloudStoragePath
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.cloud.google.batch.client.BatchConfig
+import nextflow.executor.SimpleFileCopyStrategy
+import nextflow.extension.FilesEx
+import nextflow.processor.TaskBean
+import nextflow.util.Escape
+
+/**
+ * Optional Google Batch staging when {@link BatchConfig#usesGoogleBatchStaging()} is true, honouring
+ * {@link BatchConfig#stageInCopyTransport} / {@link BatchConfig#stageOutCopyTransport} for {@code copy} modes.
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
+
+    private final BatchConfig batchConfig
+
+    GoogleBatchFileCopyStrategy(TaskBean bean, BatchConfig batchConfig) {
+        super(bean)
+        this.batchConfig = batchConfig
+    }
+
+    /**
+     * CLI stage-in when a CLI transport is selected and {@code stageInMode=copy}.
+     */
+    private boolean useCliStageInCopy() {
+        return BatchConfig.isCliCopyTransport(batchConfig.stageInCopyTransport) && 'copy' == stageinMode
+    }
+
+    private String effectiveStageOutMode() {
+        stageoutMode ?: ( workDir==targetDir ? 'copy' : 'move' )
+    }
+
+    private boolean shouldUseCliStageOutCopy() {
+        if( effectiveStageOutMode() != 'copy' )
+            return false
+        return BatchConfig.isCliCopyTransport(batchConfig.stageOutCopyTransport)
+    }
+
+    private boolean needsGoogleBatchBashLib() {
+        useCliStageInCopy() || shouldUseCliStageOutCopy()
+    }
+
+    @Override
+    String getBeforeStartScript() {
+        final base = super.getBeforeStartScript()
+        if( !needsGoogleBatchBashLib() )
+            return base
+        final gs = GoogleBatchBashLib.script(batchConfig)
+        return gs + (base ? '\n' + base : '')
+    }
+
+    @Override
+    String getStageInputFilesScript(Map<String,Path> inputFiles) {
+        if( !useCliStageInCopy() )
+            return super.getStageInputFilesScript(inputFiles)
+        def result = 'downloads=(true)\n'
+        result += super.getStageInputFilesScript(inputFiles) + '\n'
+        result += 'nxf_parallel "${downloads[@]}"\n'
+        return result
+    }
+
+    @Override
+    String stageInputFile(Path path, String targetName) {
+        if( !useCliStageInCopy() )
+            return super.stageInputFile(path, targetName)
+        final gsUri = gsUriForCliStageIn(path)
+        if( gsUri != null ) {
+            final cmd = batchConfig.maxTransferAttempts > 1
+                    ? "downloads+=(\"nxf_cp_retry nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
+                    : "downloads+=(\"nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
+            return cmd
+        }
+        return super.stageInputFile(path, targetName)
+    }
+
+    /**
+     * Resolve a {@code gs://} URI for CLI stage-in: from {@link CloudStoragePath}, or from a container fuse path under {@link GoogleBatchScriptLauncher#MOUNT_ROOT}.
+     */
+    private static String gsUriForCliStageIn(Path path) {
+        if( path instanceof CloudStoragePath )
+            return FilesEx.toUriString((CloudStoragePath)path)
+        final s = path.toString()
+        final prefix = GoogleBatchScriptLauncher.MOUNT_ROOT + '/'
+        if( s.startsWith(prefix) )
+            return toGsUriFromContainerMount(path)
+        return null
+    }
+
+    @Override
+    String getUnstageOutputFilesScript(List<String> outputFiles, Path targetDir) {
+        final mode = effectiveStageOutMode()
+        if( mode == 'move' )
+            return super.getUnstageOutputFilesScript(outputFiles, targetDir)
+        if( mode == 'copy' && shouldUseCliStageOutCopy() )
+            return getUnstageOutputFilesScriptGcloud(outputFiles, targetDir)
+        return super.getUnstageOutputFilesScript(outputFiles, targetDir)
+    }
+
+    private String getUnstageOutputFilesScriptGcloud(List<String> outputFiles, Path targetDir) {
+        final patterns = normalizeGlobStarPaths(outputFiles)
+        log.trace "[GOOGLE BATCH] Unstaging file path (CLI transport): $patterns"
+
+        if( !patterns )
+            return null
+
+        final gsTarget = toGsUriFromContainerMount(targetDir)
+        final escape = new ArrayList(outputFiles.size())
+        for( String it : patterns )
+            escape.add( Escape.path(it) )
+
+        return """\
+            uploads=()
+            IFS=\$'\\n'
+            for name in \$(eval "ls -1d ${escape.join(' ')}" | sort | uniq); do
+                uploads+=("nxf_gs_upload '\$name' '${gsTarget}' 0")
+            done
+            unset IFS
+            nxf_parallel "\${uploads[@]}"
+            """.stripIndent(true)
+    }
+
+    @Override
+    String fileStr(Path path) {
+        !useCliStageInCopy() ? super.fileStr(path) : Escape.path(path.getFileName())
+    }
+
+    @Override
+    String pipeInputFile(Path file) {
+        !useCliStageInCopy() ? super.pipeInputFile(file) : " < ${Escape.path(file.getFileName())}"
+    }
+
+    static String toGsUriFromContainerMount(Path containerPath) {
+        final s = containerPath.toString()
+        final prefix = GoogleBatchScriptLauncher.MOUNT_ROOT + '/'
+        if( !s.startsWith(prefix) )
+            throw new IllegalArgumentException("Expected path under ${GoogleBatchScriptLauncher.MOUNT_ROOT}, got: $s")
+        final rest = s.substring(prefix.length())
+        final slash = rest.indexOf('/')
+        if( slash < 0 )
+            return "gs://$rest/"
+        final bucket = rest.substring(0, slash)
+        final obj = rest.substring(slash)
+        return "gs://$bucket$obj"
+    }
+}
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
index 9db0bf9fb2..ff9b862f41 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
@@ -25,7 +25,10 @@ import com.google.cloud.storage.contrib.nio.CloudStoragePath
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.cloud.google.GoogleOpts
+import nextflow.cloud.google.batch.client.BatchConfig
 import nextflow.executor.BashWrapperBuilder
+import nextflow.executor.ScriptFileCopyStrategy
+import nextflow.executor.SimpleFileCopyStrategy
 import nextflow.extension.FilesEx
 import nextflow.processor.TaskBean
 import nextflow.processor.TaskRun
@@ -42,7 +45,7 @@ import nextflow.util.TestOnly
 @CompileStatic
 class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatchLauncherSpec {
 
-    private static final String MOUNT_ROOT = '/mnt/disks'
+    public static final String MOUNT_ROOT = '/mnt/disks'
 
     private GoogleOpts config
     private CloudStoragePath remoteWorkDir
@@ -54,8 +57,8 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
     @TestOnly
     protected GoogleBatchScriptLauncher() {}
 
-    GoogleBatchScriptLauncher(TaskBean bean, Path remoteBinDir) {
-        super(bean)
+    GoogleBatchScriptLauncher(TaskBean bean, Path remoteBinDir, BatchConfig batchConfig) {
+        super(bean, copyStrategyFor(bean, batchConfig))
         // keep track the google storage work dir
         this.remoteWorkDir = (CloudStoragePath) bean.workDir
         this.remoteBinDir = toContainerMount(remoteBinDir)
@@ -101,6 +104,12 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
             scratch = true
     }
 
+    private static ScriptFileCopyStrategy copyStrategyFor(TaskBean bean, BatchConfig batchConfig) {
+        batchConfig.usesGoogleBatchStaging()
+                ? new GoogleBatchFileCopyStrategy(bean, batchConfig)
+                : new SimpleFileCopyStrategy(bean)
+    }
+
     protected String headerScript(TaskBean bean) {
         def result = "NXF_CHDIR=${Escape.path(bean.workDir)}\n"
         if( remoteBinDir ) {
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index 792ec949d5..656f875955 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -169,7 +169,7 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         }
         else {
             final taskBean = task.toTaskBean()
-            return new GoogleBatchScriptLauncher(taskBean, executor.remoteBinDir)
+            return new GoogleBatchScriptLauncher(taskBean, executor.remoteBinDir, batchConfig)
                 .withConfig(executor.googleOpts)
                 .withIsArray(task.isArray())
         }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index b3d28343fa..3f729d2b70 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -20,9 +20,11 @@ import java.nio.file.Path
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.cloud.CloudTransferOptions
 import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
 import nextflow.script.dsl.Description
+import nextflow.util.Duration
 import nextflow.util.MemoryUnit
 /**
  * Model Google Batch config settings
@@ -33,6 +35,23 @@ import nextflow.util.MemoryUnit
 @CompileStatic
 class BatchConfig implements ConfigScope {
 
+    /**
+     * Copy via POSIX {@code cp}/links from gcsfuse paths under {@code /mnt/disks/...}.
+     */
+    static final String COPY_TRANSPORT_POSIX = 'posix'
+
+    /**
+     * Copy using {@code gcloud storage} first, then {@code gsutil}, then POSIX from the mount (see {@link nextflow.cloud.google.batch.GoogleBatchBashLib}).
+     */
+    static final String COPY_TRANSPORT_GCLOUD = 'gcloud'
+
+    /**
+     * Copy using {@code gsutil} first, then {@code gcloud storage}, then POSIX from the mount.
+     */
+    static final String COPY_TRANSPORT_GSUTIL = 'gsutil'
+
+    static final private List<String> VALID_COPY_TRANSPORTS = List.of(COPY_TRANSPORT_POSIX, COPY_TRANSPORT_GCLOUD, COPY_TRANSPORT_GSUTIL)
+
     static final private int DEFAULT_MAX_SPOT_ATTEMPTS = 0
 
     static final private List<Integer> DEFAULT_RETRY_LIST = List.of(50001)
@@ -79,6 +98,52 @@ class BatchConfig implements ConfigScope {
     """)
     final List<String> gcsfuseOptions
 
+    @ConfigOption
+    @Description("""
+        Path to the `gcloud` executable for `gcloud storage` transfers (default: `gcloud` on `PATH`).
+    """)
+    final String gcloudCli
+
+    @ConfigOption
+    @Description("""
+        Path to the `gsutil` executable (default: `gsutil` on `PATH`).
+    """)
+    final String gsutilCli
+
+    @ConfigOption
+    @Description("""
+        Maximum parallel object-storage transfers when using `gcloud` / `gsutil` staging (default: same as other cloud executors).
+    """)
+    final int maxParallelTransfers
+
+    @ConfigOption
+    @Description("""
+        Maximum retry attempts for each `gcloud` / `gsutil` transfer when using CLI-based staging.
+    """)
+    final int maxTransferAttempts
+
+    @ConfigOption
+    @Description("""
+        Delay between retry attempts for `gcloud` / `gsutil` transfers when using CLI-based staging.
+    """)
+    final Duration delayBetweenAttempts
+
+    @ConfigOption
+    @Description("""
+        When neither this nor `stageOutCopyTransport` is `gcloud` or `gsutil` (including when both are unset or only `posix`), the default is POSIX staging via {@link nextflow.executor.SimpleFileCopyStrategy} with gcsfuse mounts under `/mnt/disks`.
+
+        When set to `posix`, `gcloud`, or `gsutil`, it participates in selecting **input** copy behaviour (with `stageOutCopyTransport`). `posix` uses `cp`/links from the mount. `gcloud` / `gsutil` use the respective CLI (with fallbacks) when `process stageInMode` is `copy` (paths are under the gcsfuse mount; `gs://` URIs are derived for CLI copy). Other `stageInMode` values use the mount. Buckets remain mounted for POSIX fallback.
+    """)
+    final String stageInCopyTransport
+
+    @ConfigOption
+    @Description("""
+        When neither this nor `stageInCopyTransport` is `gcloud` or `gsutil` (including when both are unset or only `posix`), the default is POSIX staging via {@link nextflow.executor.SimpleFileCopyStrategy} with gcsfuse mounts only.
+
+        When set to `posix`, `gcloud`, or `gsutil`, it participates in selecting **output** copy behaviour (with `stageInCopyTransport`): `posix` uses POSIX from the gcsfuse mount; `gcloud` / `gsutil` use CLIs when the effective `stageOutMode` is `copy`. `move`, `rsync`, `rclone`, and `fcp` use existing wrapper behaviour (POSIX via mount). CLI-based `move` staging is not implemented.
+    """)
+    final String stageOutCopyTransport
+
     @ConfigOption
     @Description("""
     """)
@@ -152,6 +217,13 @@ class BatchConfig implements ConfigScope {
         bootDiskSize = opts.bootDiskSize as MemoryUnit
         cpuPlatform = opts.cpuPlatform
         gcsfuseOptions = opts.gcsfuseOptions as List<String> ?: DEFAULT_GCSFUSE_OPTS
+        gcloudCli = opts.gcloudCli as String
+        gsutilCli = opts.gsutilCli as String
+        maxParallelTransfers = opts.maxParallelTransfers != null ? opts.maxParallelTransfers as int : CloudTransferOptions.MAX_TRANSFER
+        maxTransferAttempts = opts.maxTransferAttempts != null ? opts.maxTransferAttempts as int : CloudTransferOptions.MAX_TRANSFER_ATTEMPTS
+        delayBetweenAttempts = opts.delayBetweenAttempts ? opts.delayBetweenAttempts as Duration : CloudTransferOptions.DEFAULT_DELAY_BETWEEN_ATTEMPTS
+        stageInCopyTransport = normaliseOptionalCopyTransport(opts.stageInCopyTransport)
+        stageOutCopyTransport = normaliseOptionalCopyTransport(opts.stageOutCopyTransport)
         installGpuDrivers = opts.installGpuDrivers as boolean
         installOpsAgent = opts.installOpsAgent as boolean
         logsPath = opts.logsPath
@@ -166,6 +238,26 @@ class BatchConfig implements ConfigScope {
         usePrivateAddress = opts.usePrivateAddress as boolean
     }
 
+    /**
+     * Load {@link nextflow.cloud.google.batch.GoogleBatchFileCopyStrategy} when any transport requests CLI object-storage copy.
+     */
+    boolean usesGoogleBatchStaging() {
+        return isCliCopyTransport(stageInCopyTransport) || isCliCopyTransport(stageOutCopyTransport)
+    }
+
+    static boolean isCliCopyTransport(String transport) {
+        return COPY_TRANSPORT_GCLOUD == transport || COPY_TRANSPORT_GSUTIL == transport
+    }
+
+    private static String normaliseOptionalCopyTransport(Object value) {
+        if( value == null )
+            return null
+        final t = value as String
+        if( !VALID_COPY_TRANSPORTS.contains(t) )
+            throw new IllegalArgumentException("Invalid google.batch copy transport: '$t' — valid values are: ${VALID_COPY_TRANSPORTS.join(', ')}")
+        return t
+    }
+
     BatchRetryConfig getRetryConfig() { retry }
 
     Path logsPath() {
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
new file mode 100644
index 0000000000..361a10a208
--- /dev/null
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
@@ -0,0 +1,127 @@
+/*
+ * Copyright 2013-2026, 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.cloud.google.batch
+
+import java.nio.file.Paths
+
+import nextflow.cloud.google.batch.client.BatchConfig
+import nextflow.processor.TaskBean
+import spock.lang.Specification
+
+class GoogleBatchFileCopyStrategyTest extends Specification {
+
+    def 'should map container mount path to gs uri' () {
+        expect:
+        GoogleBatchFileCopyStrategy.toGsUriFromContainerMount(Paths.get('/mnt/disks/mybucket/work/dir')) == 'gs://mybucket/work/dir'
+        GoogleBatchFileCopyStrategy.toGsUriFromContainerMount(Paths.get('/mnt/disks/onlybucket')) == 'gs://onlybucket/'
+    }
+
+    def 'should build gs download staging line when gcloud copy transport' () {
+        given:
+        def batch = new BatchConfig([
+            stageInCopyTransport: 'gcloud'
+        ])
+        def bean = Mock(TaskBean) {
+            getWorkDir() >> Paths.get('/mnt/disks/w/x')
+            getTargetDir() >> Paths.get('/mnt/disks/w/x')
+            getStageInMode() >> 'copy'
+        }
+        def path = Paths.get('/mnt/disks/b/data/in.txt')
+        def copy = new GoogleBatchFileCopyStrategy(bean, batch)
+
+        expect:
+        copy.stageInputFile(path, 'in.txt') == 'downloads+=("nxf_gs_download \'gs://b/data/in.txt\' in.txt")'
+    }
+
+    def 'should build gs upload unstage script' () {
+        given:
+        def batch = new BatchConfig([stageOutCopyTransport: 'gcloud'])
+        def wd = Paths.get('/mnt/disks/foo/wd')
+        def bean = Mock(TaskBean) {
+            getWorkDir() >> wd
+            getTargetDir() >> wd
+            getStageOutMode() >> null
+        }
+        def copy = new GoogleBatchFileCopyStrategy(bean, batch)
+
+        when:
+        def script = copy.getUnstageOutputFilesScript(['out.txt'], wd)
+        then:
+        script.trim() == '''
+                    uploads=()
+                    IFS=$'\\n'
+                    for name in $(eval "ls -1d out.txt" | sort | uniq); do
+                        uploads+=("nxf_gs_upload '$name' 'gs://foo/wd' 0")
+                    done
+                    unset IFS
+                    nxf_parallel "${uploads[@]}"
+                    '''
+                    .stripIndent().trim()
+    }
+
+    def 'should use posix symlink when stageIn is not cli copy' () {
+        given:
+        def batch = new BatchConfig([stageOutCopyTransport: 'gcloud'])
+        def wd = Paths.get('/mnt/disks/foo/wd')
+        def bean = Mock(TaskBean) {
+            getWorkDir() >> wd
+            getTargetDir() >> wd
+            getStageInMode() >> 'symlink'
+        }
+        def path = Paths.get('/mnt/disks/foo/bucket/data.txt')
+        def copy = new GoogleBatchFileCopyStrategy(bean, batch)
+
+        expect:
+        copy.stageInputFile(path, 'data.txt') == 'ln -s /mnt/disks/foo/bucket/data.txt data.txt'
+    }
+
+    def 'should use posix move when stageOutMode is move' () {
+        given:
+        def batch = new BatchConfig([stageOutCopyTransport: 'gcloud'])
+        def wd = Paths.get('/mnt/disks/b/work')
+        def td = Paths.get('/mnt/disks/b/out')
+        def bean = Mock(TaskBean) {
+            getWorkDir() >> wd
+            getTargetDir() >> td
+            getStageOutMode() >> 'move'
+        }
+        def copy = new GoogleBatchFileCopyStrategy(bean, batch)
+
+        when:
+        def script = copy.getUnstageOutputFilesScript(['x.txt'], td)
+        then:
+        script.contains('nxf_fs_move')
+        script.contains('/mnt/disks/b/out')
+    }
+
+    def 'should use posix copy when stageOutCopyTransport is posix' () {
+        given:
+        def batch = new BatchConfig([stageOutCopyTransport: 'posix'])
+        def wd = Paths.get('/mnt/disks/b/work')
+        def bean = Mock(TaskBean) {
+            getWorkDir() >> wd
+            getTargetDir() >> wd
+            getStageOutMode() >> 'copy'
+        }
+        def copy = new GoogleBatchFileCopyStrategy(bean, batch)
+
+        when:
+        def script = copy.getUnstageOutputFilesScript(['out.txt'], wd)
+        then:
+        script.contains('nxf_fs_copy')
+    }
+}
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy
index 13e2f7e06f..6810d11c12 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.cloud.google.batch.client
 
+import nextflow.cloud.CloudTransferOptions
+import nextflow.util.Duration
 import nextflow.util.MemoryUnit
 import spock.lang.Specification
 /**
@@ -37,6 +39,30 @@ class BatchConfigTest extends Specification {
         !config.bootDiskImage
         !config.bootDiskSize
         !config.logsPath
+        and:
+        config.maxParallelTransfers == CloudTransferOptions.MAX_TRANSFER
+        config.maxTransferAttempts == CloudTransferOptions.MAX_TRANSFER_ATTEMPTS
+        config.delayBetweenAttempts == CloudTransferOptions.DEFAULT_DELAY_BETWEEN_ATTEMPTS
+        !config.gcloudCli
+        !config.gsutilCli
+        and:
+        !config.stageInCopyTransport
+        !config.stageOutCopyTransport
+        !config.usesGoogleBatchStaging()
+    }
+
+    def 'should reject invalid copy transport' () {
+        when:
+        new BatchConfig([stageInCopyTransport: 'ftp'])
+        then:
+        thrown(IllegalArgumentException)
+    }
+
+    def 'should detect google batch staging when cli transport set' () {
+        expect:
+        new BatchConfig([stageOutCopyTransport: 'gcloud']).usesGoogleBatchStaging()
+        new BatchConfig([stageInCopyTransport: 'gsutil']).usesGoogleBatchStaging()
+        !new BatchConfig([stageInCopyTransport: 'posix']).usesGoogleBatchStaging()
     }
 
     def 'should create batch config with custom settings' () {
@@ -49,7 +75,13 @@ class BatchConfigTest extends Specification {
             bootDiskImage: 'batch-foo',
             bootDiskSize: '100GB',
             logsPath: 'gs://my-logs-bucket/logs',
-            installOpsAgent: true
+            installOpsAgent: true,
+            stageInCopyTransport: 'gcloud',
+            stageOutCopyTransport: 'posix',
+            gcloudCli: '/opt/google/gcloud',
+            maxParallelTransfers: 8,
+            maxTransferAttempts: 3,
+            delayBetweenAttempts: '5s'
         ]
 
         when:
@@ -67,6 +99,13 @@ class BatchConfigTest extends Specification {
         config.logsPath == 'gs://my-logs-bucket/logs'
         and:
         config.installOpsAgent == true
+        and:
+        config.stageInCopyTransport == 'gcloud'
+        config.stageOutCopyTransport == 'posix'
+        config.gcloudCli == '/opt/google/gcloud'
+        config.maxParallelTransfers == 8
+        config.maxTransferAttempts == 3
+        config.delayBetweenAttempts == Duration.of('5s')
     }
 
 }

From 2dc467241ad34df8933c523652d4945682384272 Mon Sep 17 00:00:00 2001
From: Tomiles <116039+tomiles@users.noreply.github.com>
Date: Thu, 2 Apr 2026 23:21:19 +0200
Subject: [PATCH 2/6] feat(nf-google): some optimizations based on review

Signed-off-by: Tomiles <116039+tomiles@users.noreply.github.com>
---
 .../google/batch/GoogleBatchBashLib.groovy    | 82 ++++++-------------
 .../batch/GoogleBatchFileCopyStrategy.groovy  | 15 ++--
 .../google/batch/client/BatchConfig.groovy    | 54 ++++++------
 .../GoogleBatchFileCopyStrategyTest.groovy    |  4 +-
 4 files changed, 59 insertions(+), 96 deletions(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy
index 619998a082..01bf04943f 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchBashLib.groovy
@@ -123,7 +123,8 @@ class GoogleBatchBashLib extends BashFunLib<GoogleBatchBashLib> {
             [[ -n "\$ms" ]] || return 1
             [[ -e "\$ms" || -d "\$ms" ]] || return 1
             mkdir -p "\$(dirname "\$target")"
-            cp -fRL "\$ms" "\$target"
+            cp -fRL "\$ms" "\$target" || return 1
+            return 0
         }
 
         nxf_gs_download() {
@@ -145,20 +146,17 @@ class GoogleBatchBashLib extends BashFunLib<GoogleBatchBashLib> {
                 ;;
             esac
             >&2 echo "Unable to download path: \$source"
-            exit 1
+            return 1
         }
 
         nxf_gs_upload_try_gcloud() {
             command -v "\$NXF_GCLOUD" >/dev/null 2>&1 || return 1
             local name=\$1
             local gspath=\$2
-            if [[ "\$name" == '-' ]]; then
-                return 1
-            fi
             if [[ -d "\$name" ]]; then
-                \$NXF_GCLOUD storage cp --recursive "\$name" "\$gspath/\$name"
+                \$NXF_GCLOUD storage cp --recursive "\$name" "\$gspath/\$name" || return 1
             else
-                \$NXF_GCLOUD storage cp "\$name" "\$gspath/\$name"
+                \$NXF_GCLOUD storage cp "\$name" "\$gspath/\$name" || return 1
             fi
         }
 
@@ -166,73 +164,43 @@ class GoogleBatchBashLib extends BashFunLib<GoogleBatchBashLib> {
             command -v "\$NXF_GSUTIL" >/dev/null 2>&1 || return 1
             local name=\$1
             local gspath=\$2
-            if [[ "\$name" == '-' ]]; then
-                return 1
-            fi
             if [[ -d "\$name" ]]; then
-                \$NXF_GSUTIL -m cp -r "\$name" "\$gspath/\$name"
+                \$NXF_GSUTIL -m cp -r "\$name" "\$gspath/\$name" || return 1
             else
-                \$NXF_GSUTIL cp "\$name" "\$gspath/\$name"
+                \$NXF_GSUTIL cp "\$name" "\$gspath/\$name" || return 1
             fi
         }
 
         nxf_gs_upload_try_mount() {
             local name=\$1
             local gspath=\$2
-            if [[ "\$name" == '-' ]]; then
-                return 1
-            fi
             local dest
             dest=\$(nxf_gs_uri_to_mount "\$gspath/\$name")
             [[ -n "\$dest" ]] || return 1
             mkdir -p "\$(dirname "\$dest")"
-            cp -fRL "\$name" "\$dest"
+            cp -fRL "\$name" "\$dest" || return 1
         }
 
         nxf_gs_upload() {
             local name=\$1
             local gspath=\${2%/}
-            local move=\${3:-0}
-            if [[ "\$name" == '-' ]]; then
-                if command -v "\$NXF_GCLOUD" >/dev/null 2>&1 && \$NXF_GCLOUD storage cp - "\$gspath"; then
-                    :
-                elif command -v "\$NXF_GSUTIL" >/dev/null 2>&1 && \$NXF_GSUTIL cp - "\$gspath"; then
-                    :
-                else
-                    return 1
-                fi
-            else
-                case "\${NXF_STAGE_OUT_COPY_TRANSPORT:-posix}" in
-                gsutil)
-                    if nxf_gs_upload_try_gsutil "\$name" "\$gspath"; then :;
-                    elif nxf_gs_upload_try_gcloud "\$name" "\$gspath"; then :;
-                    elif nxf_gs_upload_try_mount "\$name" "\$gspath"; then :;
-                    else
-                        >&2 echo "Unable to upload path: \$name"
-                        return 1
-                    fi
-                    ;;
-                gcloud)
-                    if nxf_gs_upload_try_gcloud "\$name" "\$gspath"; then :;
-                    elif nxf_gs_upload_try_gsutil "\$name" "\$gspath"; then :;
-                    elif nxf_gs_upload_try_mount "\$name" "\$gspath"; then :;
-                    else
-                        >&2 echo "Unable to upload path: \$name"
-                        return 1
-                    fi
-                    ;;
-                posix|*)
-                    if nxf_gs_upload_try_mount "\$name" "\$gspath"; then :;
-                    else
-                        >&2 echo "Unable to upload path: \$name"
-                        return 1
-                    fi
-                    ;;
-                esac
-            fi
-            if [[ "\$move" == "1" && "\$name" != '-' ]]; then
-                rm -rf "\$name"
-            fi
+            case "\${NXF_STAGE_OUT_COPY_TRANSPORT:-posix}" in
+            gsutil)
+                if nxf_gs_upload_try_gsutil "\$name" "\$gspath"; then return 0; fi
+                if nxf_gs_upload_try_gcloud "\$name" "\$gspath"; then return 0; fi
+                if nxf_gs_upload_try_mount "\$name" "\$gspath"; then return 0; fi
+                ;;
+            gcloud)
+                if nxf_gs_upload_try_gcloud "\$name" "\$gspath"; then return 0; fi
+                if nxf_gs_upload_try_gsutil "\$name" "\$gspath"; then return 0; fi
+                if nxf_gs_upload_try_mount "\$name" "\$gspath"; then return 0; fi
+                ;;
+            posix|*)
+                if nxf_gs_upload_try_mount "\$name" "\$gspath"; then return 0; fi
+                ;;
+            esac
+            >&2 echo "Unable to upload path: \$name"
+            return 1
         }
         """.stripIndent(true)
     }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
index 891355d44a..19c7d5f9d1 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
@@ -48,7 +48,7 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      * CLI stage-in when a CLI transport is selected and {@code stageInMode=copy}.
      */
     private boolean useCliStageInCopy() {
-        return BatchConfig.isCliCopyTransport(batchConfig.stageInCopyTransport) && 'copy' == stageinMode
+        return batchConfig.stageInCopyTransport in [BatchConfig.COPY_TRANSPORT_GCLOUD, BatchConfig.COPY_TRANSPORT_GSUTIL] && 'copy' == stageinMode
     }
 
     private String effectiveStageOutMode() {
@@ -58,7 +58,7 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
     private boolean shouldUseCliStageOutCopy() {
         if( effectiveStageOutMode() != 'copy' )
             return false
-        return BatchConfig.isCliCopyTransport(batchConfig.stageOutCopyTransport)
+        return batchConfig.stageOutCopyTransport in [BatchConfig.COPY_TRANSPORT_GCLOUD, BatchConfig.COPY_TRANSPORT_GSUTIL]
     }
 
     private boolean needsGoogleBatchBashLib() {
@@ -90,10 +90,7 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
             return super.stageInputFile(path, targetName)
         final gsUri = gsUriForCliStageIn(path)
         if( gsUri != null ) {
-            final cmd = batchConfig.maxTransferAttempts > 1
-                    ? "downloads+=(\"nxf_cp_retry nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
-                    : "downloads+=(\"nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
-            return cmd
+            return "downloads+=(\"nxf_cp_retry nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
         }
         return super.stageInputFile(path, targetName)
     }
@@ -117,11 +114,11 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
         if( mode == 'move' )
             return super.getUnstageOutputFilesScript(outputFiles, targetDir)
         if( mode == 'copy' && shouldUseCliStageOutCopy() )
-            return getUnstageOutputFilesScriptGcloud(outputFiles, targetDir)
+            return getUnstageOutputFilesScriptCli(outputFiles, targetDir)
         return super.getUnstageOutputFilesScript(outputFiles, targetDir)
     }
 
-    private String getUnstageOutputFilesScriptGcloud(List<String> outputFiles, Path targetDir) {
+    private String getUnstageOutputFilesScriptCli(List<String> outputFiles, Path targetDir) {
         final patterns = normalizeGlobStarPaths(outputFiles)
         log.trace "[GOOGLE BATCH] Unstaging file path (CLI transport): $patterns"
 
@@ -137,7 +134,7 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
             uploads=()
             IFS=\$'\\n'
             for name in \$(eval "ls -1d ${escape.join(' ')}" | sort | uniq); do
-                uploads+=("nxf_gs_upload '\$name' '${gsTarget}' 0")
+                uploads+=("nxf_gs_upload '\$name' '${gsTarget}'")
             done
             unset IFS
             nxf_parallel "\${uploads[@]}"
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index 3f729d2b70..44ef686a22 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -27,7 +27,18 @@ import nextflow.script.dsl.Description
 import nextflow.util.Duration
 import nextflow.util.MemoryUnit
 /**
- * Model Google Batch config settings
+ * Model Google Batch config settings.
+ * <p>
+ * <strong>Copy transports</strong> ({@link #stageInCopyTransport}, {@link #stageOutCopyTransport}): optional values
+ * {@code posix}, {@code gcloud}, {@code gsutil}. When unset or only {@code posix}, staging uses
+ * {@link nextflow.executor.SimpleFileCopyStrategy} with gcsfuse paths under {@code /mnt/disks}. When {@code gcloud}
+ * or {@code gsutil} is set for a direction, {@link nextflow.cloud.google.batch.GoogleBatchFileCopyStrategy} loads and
+ * generated bash uses {@code gcloud storage} / {@code gsutil} with fallbacks to POSIX copy from the mount; order is
+ * chosen per transport (see {@link nextflow.cloud.google.batch.GoogleBatchBashLib}). CLI stage-in applies when
+ * {@code process stageInMode} is {@code copy}; CLI stage-out when effective {@code stageOutMode} is {@code copy}.
+ * {@code move} / {@code rsync} / etc. keep existing POSIX behaviour. Parallelism and retries use
+ * {@link #maxParallelTransfers}, {@link #maxTransferAttempts}, {@link #delayBetweenAttempts} with {@code nxf_parallel}
+ * / {@code nxf_cp_retry} in the task script.
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
@@ -100,47 +111,43 @@ class BatchConfig implements ConfigScope {
 
     @ConfigOption
     @Description("""
-        Path to the `gcloud` executable for `gcloud storage` transfers (default: `gcloud` on `PATH`).
+        `gcloud` executable path (default: `gcloud` on `PATH`).
     """)
     final String gcloudCli
 
     @ConfigOption
     @Description("""
-        Path to the `gsutil` executable (default: `gsutil` on `PATH`).
+        `gsutil` executable path (default: `gsutil` on `PATH`).
     """)
     final String gsutilCli
 
     @ConfigOption
     @Description("""
-        Maximum parallel object-storage transfers when using `gcloud` / `gsutil` staging (default: same as other cloud executors).
+        Max parallel CLI object copies (default: same as other cloud executors).
     """)
     final int maxParallelTransfers
 
     @ConfigOption
     @Description("""
-        Maximum retry attempts for each `gcloud` / `gsutil` transfer when using CLI-based staging.
+        Max retries per CLI copy (default: same as other cloud executors).
     """)
     final int maxTransferAttempts
 
     @ConfigOption
     @Description("""
-        Delay between retry attempts for `gcloud` / `gsutil` transfers when using CLI-based staging.
+        Delay between CLI copy retries (default: same as other cloud executors).
     """)
     final Duration delayBetweenAttempts
 
     @ConfigOption
     @Description("""
-        When neither this nor `stageOutCopyTransport` is `gcloud` or `gsutil` (including when both are unset or only `posix`), the default is POSIX staging via {@link nextflow.executor.SimpleFileCopyStrategy} with gcsfuse mounts under `/mnt/disks`.
-
-        When set to `posix`, `gcloud`, or `gsutil`, it participates in selecting **input** copy behaviour (with `stageOutCopyTransport`). `posix` uses `cp`/links from the mount. `gcloud` / `gsutil` use the respective CLI (with fallbacks) when `process stageInMode` is `copy` (paths are under the gcsfuse mount; `gs://` URIs are derived for CLI copy). Other `stageInMode` values use the mount. Buckets remain mounted for POSIX fallback.
+        Stage-in copy transport: `posix`, `gcloud`, or `gsutil`.
     """)
     final String stageInCopyTransport
 
     @ConfigOption
     @Description("""
-        When neither this nor `stageInCopyTransport` is `gcloud` or `gsutil` (including when both are unset or only `posix`), the default is POSIX staging via {@link nextflow.executor.SimpleFileCopyStrategy} with gcsfuse mounts only.
-
-        When set to `posix`, `gcloud`, or `gsutil`, it participates in selecting **output** copy behaviour (with `stageInCopyTransport`): `posix` uses POSIX from the gcsfuse mount; `gcloud` / `gsutil` use CLIs when the effective `stageOutMode` is `copy`. `move`, `rsync`, `rclone`, and `fcp` use existing wrapper behaviour (POSIX via mount). CLI-based `move` staging is not implemented.
+        Stage-out copy transport: `posix`, `gcloud`, or `gsutil`.
     """)
     final String stageOutCopyTransport
 
@@ -222,8 +229,12 @@ class BatchConfig implements ConfigScope {
         maxParallelTransfers = opts.maxParallelTransfers != null ? opts.maxParallelTransfers as int : CloudTransferOptions.MAX_TRANSFER
         maxTransferAttempts = opts.maxTransferAttempts != null ? opts.maxTransferAttempts as int : CloudTransferOptions.MAX_TRANSFER_ATTEMPTS
         delayBetweenAttempts = opts.delayBetweenAttempts ? opts.delayBetweenAttempts as Duration : CloudTransferOptions.DEFAULT_DELAY_BETWEEN_ATTEMPTS
-        stageInCopyTransport = normaliseOptionalCopyTransport(opts.stageInCopyTransport)
-        stageOutCopyTransport = normaliseOptionalCopyTransport(opts.stageOutCopyTransport)
+        stageInCopyTransport = opts.stageInCopyTransport as String
+        stageOutCopyTransport = opts.stageOutCopyTransport as String
+        for (String t in [stageInCopyTransport, stageOutCopyTransport]) {
+            if (t && t !in VALID_COPY_TRANSPORTS)
+                throw new IllegalArgumentException("Invalid google.batch copy transport: '$t' — valid values are: ${VALID_COPY_TRANSPORTS.join(', ')}")
+        }
         installGpuDrivers = opts.installGpuDrivers as boolean
         installOpsAgent = opts.installOpsAgent as boolean
         logsPath = opts.logsPath
@@ -242,20 +253,7 @@ class BatchConfig implements ConfigScope {
      * Load {@link nextflow.cloud.google.batch.GoogleBatchFileCopyStrategy} when any transport requests CLI object-storage copy.
      */
     boolean usesGoogleBatchStaging() {
-        return isCliCopyTransport(stageInCopyTransport) || isCliCopyTransport(stageOutCopyTransport)
-    }
-
-    static boolean isCliCopyTransport(String transport) {
-        return COPY_TRANSPORT_GCLOUD == transport || COPY_TRANSPORT_GSUTIL == transport
-    }
-
-    private static String normaliseOptionalCopyTransport(Object value) {
-        if( value == null )
-            return null
-        final t = value as String
-        if( !VALID_COPY_TRANSPORTS.contains(t) )
-            throw new IllegalArgumentException("Invalid google.batch copy transport: '$t' — valid values are: ${VALID_COPY_TRANSPORTS.join(', ')}")
-        return t
+        return [stageInCopyTransport, stageOutCopyTransport].any { it in [COPY_TRANSPORT_GCLOUD, COPY_TRANSPORT_GSUTIL] }
     }
 
     BatchRetryConfig getRetryConfig() { retry }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
index 361a10a208..7e62e88120 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
@@ -44,7 +44,7 @@ class GoogleBatchFileCopyStrategyTest extends Specification {
         def copy = new GoogleBatchFileCopyStrategy(bean, batch)
 
         expect:
-        copy.stageInputFile(path, 'in.txt') == 'downloads+=("nxf_gs_download \'gs://b/data/in.txt\' in.txt")'
+        copy.stageInputFile(path, 'in.txt') == 'downloads+=("nxf_cp_retry nxf_gs_download \'gs://b/data/in.txt\' in.txt")'
     }
 
     def 'should build gs upload unstage script' () {
@@ -65,7 +65,7 @@ class GoogleBatchFileCopyStrategyTest extends Specification {
                     uploads=()
                     IFS=$'\\n'
                     for name in $(eval "ls -1d out.txt" | sort | uniq); do
-                        uploads+=("nxf_gs_upload '$name' 'gs://foo/wd' 0")
+                        uploads+=("nxf_gs_upload '$name' 'gs://foo/wd'")
                     done
                     unset IFS
                     nxf_parallel "${uploads[@]}"

From c0e3c0960fc8b965c01f8c02ea89cc3c46babdf9 Mon Sep 17 00:00:00 2001
From: Tomiles <116039+tomiles@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:53:13 +0200
Subject: [PATCH 3/6] feat(nf-google): make the retry behaviour more
 consistent, and centralized CLI transport detection

Signed-off-by: Tomiles <116039+tomiles@users.noreply.github.com>
---
 .../batch/GoogleBatchFileCopyStrategy.groovy   |  8 +++++---
 .../google/batch/client/BatchConfig.groovy     |  7 ++++++-
 .../GoogleBatchFileCopyStrategyTest.groovy     | 18 ++++++++++++++++++
 3 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
index 19c7d5f9d1..c4471d8af6 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategy.groovy
@@ -48,7 +48,7 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      * CLI stage-in when a CLI transport is selected and {@code stageInMode=copy}.
      */
     private boolean useCliStageInCopy() {
-        return batchConfig.stageInCopyTransport in [BatchConfig.COPY_TRANSPORT_GCLOUD, BatchConfig.COPY_TRANSPORT_GSUTIL] && 'copy' == stageinMode
+        return BatchConfig.isCliCopyTransport(batchConfig.stageInCopyTransport) && 'copy' == stageinMode
     }
 
     private String effectiveStageOutMode() {
@@ -58,7 +58,7 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
     private boolean shouldUseCliStageOutCopy() {
         if( effectiveStageOutMode() != 'copy' )
             return false
-        return batchConfig.stageOutCopyTransport in [BatchConfig.COPY_TRANSPORT_GCLOUD, BatchConfig.COPY_TRANSPORT_GSUTIL]
+        return BatchConfig.isCliCopyTransport(batchConfig.stageOutCopyTransport)
     }
 
     private boolean needsGoogleBatchBashLib() {
@@ -90,7 +90,9 @@ class GoogleBatchFileCopyStrategy extends SimpleFileCopyStrategy {
             return super.stageInputFile(path, targetName)
         final gsUri = gsUriForCliStageIn(path)
         if( gsUri != null ) {
-            return "downloads+=(\"nxf_cp_retry nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
+            return batchConfig.maxTransferAttempts > 1
+                    ? "downloads+=(\"nxf_cp_retry nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
+                    : "downloads+=(\"nxf_gs_download '${gsUri}' ${Escape.path(targetName)}\")"
         }
         return super.stageInputFile(path, targetName)
     }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index 44ef686a22..b2cf7bba04 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -62,6 +62,7 @@ class BatchConfig implements ConfigScope {
     static final String COPY_TRANSPORT_GSUTIL = 'gsutil'
 
     static final private List<String> VALID_COPY_TRANSPORTS = List.of(COPY_TRANSPORT_POSIX, COPY_TRANSPORT_GCLOUD, COPY_TRANSPORT_GSUTIL)
+    static final private List<String> CLI_COPY_TRANSPORTS = List.of(COPY_TRANSPORT_GCLOUD, COPY_TRANSPORT_GSUTIL)
 
     static final private int DEFAULT_MAX_SPOT_ATTEMPTS = 0
 
@@ -253,7 +254,11 @@ class BatchConfig implements ConfigScope {
      * Load {@link nextflow.cloud.google.batch.GoogleBatchFileCopyStrategy} when any transport requests CLI object-storage copy.
      */
     boolean usesGoogleBatchStaging() {
-        return [stageInCopyTransport, stageOutCopyTransport].any { it in [COPY_TRANSPORT_GCLOUD, COPY_TRANSPORT_GSUTIL] }
+        return [stageInCopyTransport, stageOutCopyTransport].any { isCliCopyTransport(it) }
+    }
+
+    static boolean isCliCopyTransport(String transport) {
+        return transport in CLI_COPY_TRANSPORTS
     }
 
     BatchRetryConfig getRetryConfig() { retry }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
index 7e62e88120..a5642e791e 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchFileCopyStrategyTest.groovy
@@ -43,6 +43,24 @@ class GoogleBatchFileCopyStrategyTest extends Specification {
         def path = Paths.get('/mnt/disks/b/data/in.txt')
         def copy = new GoogleBatchFileCopyStrategy(bean, batch)
 
+        expect:
+        copy.stageInputFile(path, 'in.txt') == 'downloads+=("nxf_gs_download \'gs://b/data/in.txt\' in.txt")'
+    }
+
+    def 'should build gs download staging line with retry when maxTransferAttempts > 1' () {
+        given:
+        def batch = new BatchConfig([
+            stageInCopyTransport: 'gcloud',
+            maxTransferAttempts: 3
+        ])
+        def bean = Mock(TaskBean) {
+            getWorkDir() >> Paths.get('/mnt/disks/w/x')
+            getTargetDir() >> Paths.get('/mnt/disks/w/x')
+            getStageInMode() >> 'copy'
+        }
+        def path = Paths.get('/mnt/disks/b/data/in.txt')
+        def copy = new GoogleBatchFileCopyStrategy(bean, batch)
+
         expect:
         copy.stageInputFile(path, 'in.txt') == 'downloads+=("nxf_cp_retry nxf_gs_download \'gs://b/data/in.txt\' in.txt")'
     }

From caf8f541be5e15c81361d06bb84a3c7f5f15e809 Mon Sep 17 00:00:00 2001
From: Tomiles <116039+tomiles@users.noreply.github.com>
Date: Tue, 14 Apr 2026 11:23:31 +0200
Subject: [PATCH 4/6] feat(nf-google): fold in #6917 that defaults to copy
 stageout mode

Signed-off-by: Tomiles <116039+tomiles@users.noreply.github.com>
---
 .../batch/GoogleBatchScriptLauncher.groovy    |  4 ++++
 .../GoogleBatchScriptLauncherTest.groovy      | 20 ++++++++++++++++++-
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
index ff9b862f41..6efa60a7fd 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
@@ -58,6 +58,10 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
     protected GoogleBatchScriptLauncher() {}
 
     GoogleBatchScriptLauncher(TaskBean bean, Path remoteBinDir, BatchConfig batchConfig) {
+        // Unstaging is cross-device on Google Batch (gcsfuse-mounted work dir).
+        // `move` can fail with overlapping outputs or symlinked paths.
+        if( bean.stageOutMode == null )
+            bean.stageOutMode = 'copy'
         super(bean, copyStrategyFor(bean, batchConfig))
         // keep track the google storage work dir
         this.remoteWorkDir = (CloudStoragePath) bean.workDir
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy
index 1982722518..d833de90c5 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy
@@ -17,10 +17,10 @@
 package nextflow.cloud.google.batch
 
 import java.nio.file.Paths
-
 import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem
 import nextflow.cloud.google.GoogleOpts
 import nextflow.cloud.google.batch.client.BatchConfig
+import nextflow.processor.TaskBean
 import nextflow.processor.TaskRun
 import spock.lang.Specification
 import spock.lang.Unroll
@@ -87,6 +87,24 @@ class GoogleBatchScriptLauncherTest extends Specification{
         volumes[1].getMountOptionsList() == ['-o rw', '-implicit-dirs', '-o allow_other', '--uid=1000', '--billing-project my-project']
     }
 
+    def 'should default stageOutMode to copy when not set' () {
+        given:
+        def workDir = CloudStorageFileSystem.forBucket('foo').getPath('/scratch')
+        def targetDir = CloudStorageFileSystem.forBucket('foo').getPath('/scratch')
+        def bean = new TaskBean(
+                workDir: workDir,
+                targetDir: targetDir,
+                stageOutMode: null,
+                inputFiles: [:]
+        )
+
+        when:
+        new GoogleBatchScriptLauncher(bean, null, Mock(BatchConfig))
+
+        then:
+        bean.stageOutMode == 'copy'
+    }
+
     def 'should return target files in remote work dir' () {
         given:
         def launcher = new GoogleBatchScriptLauncher()

From 03e2f1a79bb38fcd7198880d5c5ba19e3932688e Mon Sep 17 00:00:00 2001
From: Tomiles <116039+tomiles@users.noreply.github.com>
Date: Tue, 14 Apr 2026 11:36:35 +0200
Subject: [PATCH 5/6] feat(nf-google): document changes

Signed-off-by: Tomiles <116039+tomiles@users.noreply.github.com>
---
 docs/google.md           | 16 ++++++++++++++++
 docs/reference/config.md | 24 ++++++++++++++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/docs/google.md b/docs/google.md
index d2188a4e8f..c3dfdafbe9 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -88,6 +88,22 @@ Notes:
 - A container image must be specified to execute processes. You can use a different Docker image for each process using one or more {ref}`config-process-selectors`.
 - Make sure to specify the project ID, not the project name.
 - Make sure to specify a location where Google Batch is available. Refer to the [Google Batch documentation](https://cloud.google.com/batch/docs/get-started#locations) for region availability.
+- By default, Google Batch output unstaging uses `copy` when `stageOutMode` is not set, because unstaging goes from local scratch to a gcsfuse-mounted work directory and `move` can fail with overlapping outputs or symlinked paths.
+
+Optional transfer settings:
+
+```groovy
+google {
+    batch {
+        // Default is 'posix' when unset
+        stageInCopyTransport = 'gcloud'   // or 'gsutil' / 'posix'
+        stageOutCopyTransport = 'gcloud'  // or 'gsutil' / 'posix'
+    }
+}
+```
+
+When `gcloud` or `gsutil` is selected, CLI staging is used for `copy` mode with fallback to POSIX mount copy.
+Users are responsible for ensuring the selected CLI transport is available in the task container/runtime environment.
 
 Read the {ref}`Google configuration<config-google>` section to learn more about advanced configuration options.
 
diff --git a/docs/reference/config.md b/docs/reference/config.md
index 7519a4fe9f..a9f51191fc 100644
--- a/docs/reference/config.md
+++ b/docs/reference/config.md
@@ -960,11 +960,20 @@ The following settings are available:
 `google.batch.cpuPlatform`
 : The [minimum CPU Platform](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications), e.g. `'Intel Skylake'` (default: none).
 
+`google.batch.delayBetweenAttempts`
+: Delay between transfer retry attempts (default: `10 sec`).
+
+`google.batch.gcloudCli`
+: The `gcloud` executable path used for CLI staging (default: `gcloud` from `PATH`).
+
 `google.batch.gcsfuseOptions`
 : :::{versionadded} 25.03.0-edge
   :::
 : List of custom mount options for `gcsfuse` (default: `['-o rw', '-implicit-dirs']`).
 
+`google.batch.gsutilCli`
+: The `gsutil` executable path used for CLI staging (default: `gsutil` from `PATH`).
+
 `google.batch.installOpsAgent`
 : Enables Ops Agent installation on Google Batch instances for enhanced monitoring and logging (default: `false`). See the [Google Batch documentation](https://docs.cloud.google.com/batch/docs/create-run-job-ops-agent) for details.
 
@@ -987,6 +996,12 @@ The following settings are available:
 : Max number of execution attempts of a job interrupted by a Compute Engine Spot reclaim event (default: `0`).
 : See also: `google.batch.autoRetryExitCodes`
 
+`google.batch.maxParallelTransfers`
+: Max parallel upload/download transfer operations per task script (default: `4`).
+
+`google.batch.maxTransferAttempts`
+: Max transfer retry attempts used by built-in transfer retry wrappers (default: `1`).
+
 `google.batch.network`
 : The URL of an existing network resource to which the VM will be attached.
 
@@ -1007,6 +1022,15 @@ The following settings are available:
 `google.batch.spot`
 : Enable the use of spot virtual machines (default: `false`).
 
+`google.batch.stageInCopyTransport`
+: Stage-in transport for `copy` mode. Can be `posix`, `gcloud`, or `gsutil` (default: `posix`).
+: When set to `gcloud` or `gsutil`, CLI staging is used with fallback to POSIX mount copy.
+
+`google.batch.stageOutCopyTransport`
+: Stage-out transport for `copy` mode. Can be `posix`, `gcloud`, or `gsutil` (default: `posix`).
+: When set to `gcloud` or `gsutil`, CLI staging is used with fallback to POSIX mount copy.
+: Users are responsible for ensuring the selected CLI transport is available in the task runtime/container environment.
+
 `google.batch.subnetwork`
 : The URL of an existing subnetwork resource in the network to which the VM will be attached.
 

From b48e88675ed700f51c47dad16063964cd79c2b25 Mon Sep 17 00:00:00 2001
From: Tomiles <116039+tomiles@users.noreply.github.com>
Date: Tue, 14 Apr 2026 11:51:56 +0200
Subject: [PATCH 6/6] feat(nf-google): fixes for failing tests

Signed-off-by: Tomiles <116039+tomiles@users.noreply.github.com>
---
 .../google/batch/GoogleBatchScriptLauncher.groovy  | 14 +++++++++-----
 .../cloud/google/batch/client/BatchConfig.groovy   |  2 +-
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
index 6efa60a7fd..feda0aedd9 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
@@ -58,11 +58,7 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
     protected GoogleBatchScriptLauncher() {}
 
     GoogleBatchScriptLauncher(TaskBean bean, Path remoteBinDir, BatchConfig batchConfig) {
-        // Unstaging is cross-device on Google Batch (gcsfuse-mounted work dir).
-        // `move` can fail with overlapping outputs or symlinked paths.
-        if( bean.stageOutMode == null )
-            bean.stageOutMode = 'copy'
-        super(bean, copyStrategyFor(bean, batchConfig))
+        super(defaultStageOutMode(bean), copyStrategyFor(bean, batchConfig))
         // keep track the google storage work dir
         this.remoteWorkDir = (CloudStoragePath) bean.workDir
         this.remoteBinDir = toContainerMount(remoteBinDir)
@@ -114,6 +110,14 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
                 : new SimpleFileCopyStrategy(bean)
     }
 
+    private static TaskBean defaultStageOutMode(TaskBean bean) {
+        // Unstaging is cross-device on Google Batch (gcsfuse-mounted work dir).
+        // `move` can fail with overlapping outputs or symlinked paths.
+        if( bean.stageOutMode == null )
+            bean.stageOutMode = 'copy'
+        return bean
+    }
+
     protected String headerScript(TaskBean bean) {
         def result = "NXF_CHDIR=${Escape.path(bean.workDir)}\n"
         if( remoteBinDir ) {
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index b2cf7bba04..8fc07bab80 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -258,7 +258,7 @@ class BatchConfig implements ConfigScope {
     }
 
     static boolean isCliCopyTransport(String transport) {
-        return transport in CLI_COPY_TRANSPORTS
+        return transport != null && transport in CLI_COPY_TRANSPORTS
     }
 
     BatchRetryConfig getRetryConfig() { retry }