diff --git a/src/runner/main.nf b/src/runner/main.nf
index a97a5bd..5b77f7c 100644
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -1,8 +1,14 @@
-def date = new Date().format('yyyyMMdd_hhmmss')
+import java.util.concurrent.ThreadPoolExecutor
+import java.util.concurrent.atomic.AtomicBoolean
 
+def date = new Date().format('yyyyMMdd_hhmmss')
 def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
+session = nextflow.Nextflow.getSession()
+final service = session.publishDirExecutorService()
+
+
 workflow run_wf {
   take:
     input_ch
@@ -51,13 +57,16 @@ workflow run_wf {
           state + result + [ to_return: result ]
         },
       )
-      | publish.run(
-        fromState: { id, state ->
-          println(state.plain_output)
+      | map {id, state ->
           def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
           def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"
-
           def prefix = (id2 == "run") ? "" : "${id2}/"
+          def new_state = state + ["prefix": prefix]
+          [id, new_state]
+      }
+      | publish.run(
+        fromState: { id, state ->
+          def prefix = state.prefix
           // These output names are determined by arguments.
           def fastq_output_1 = "${prefix}${state.fastq_output_workflow}"
           def sample_qc_output_1 = "${prefix}${state.sample_qc_output_workflow}"
@@ -67,18 +76,6 @@ workflow run_wf {
           def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
 
           println("Publising to ${params.publish_dir}/${prefix}")
-
-          // Create a file to indicate that the publishing (transfer) of files has been completed.
-          // Multiple items can be added to onCompleteActions; which is required when processing multiple sequencing runs at a time.
-          // Alternatively setOnComplete could be used to add actions, but that only adds them at the end of the list (which is executed in order).
-          // The 'completed.txt' file must be created before the onComplete of the integration tests are run, so we need to prepend to the list.
-          workflow.onCompleteActions.add(0, {
-            if (workflow.exitStatus == 0) { 
-              def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt")
-              complete_file.text = "" // This will create a file when it does not exist.
-            }
-          })
-
           [
             input: state.output,
             input_sample_qc: state.output_sample_qc,
@@ -92,7 +89,7 @@ workflow run_wf {
             output_demultiplexer_logs: demultiplexer_logs_output,
           ]
         },
-        toState: { id, result, state -> [ fastq_output: state.to_return.output ] },
+        toState: { id, result, state -> [ "fastq_output": state.to_return.output, "prefix": state.prefix ] },
         directives: [
           publishDir: [
             path: "${params.publish_dir}", 
@@ -102,8 +99,60 @@ workflow run_wf {
         ]
       )
 
+has_published = new AtomicBoolean(false)
+
+interval_ch = channel.interval('10s'){ i ->
+  // Allow this channel to stop generating events based on a later signal
+  if (has_published.get()) {
+    return channel.STOP
+  }
+  i
+}
+
+await_ch = output_ch
+  // Wait for demultiplexing processes to be done
+  | toSortedList()
+  // Create periodic events in order to check for the publishing to be done
+  | combine(interval_ch)
+  | until { event ->
+    println("Checking if publishing has finished in service ${service}")
+    def running_tasks = null
+    if(service instanceof ThreadPoolExecutor) {
+      def completed_tasks = service.getCompletedTaskCount()
+      def task_count = service.getTaskCount()
+      running_tasks = completed_tasks - task_count
+    }
+    else if( System.getenv('NXF_ENABLE_VIRTUAL_THREADS') ) {
+      running_tasks = service.threadCount()
+    }
+    else {
+      error("Publishing service of class ${service.getClass()} is not supported.")
+    }
+    
+    if (running_tasks == 0) {
+      println("Publishing has finished all current tasks. Continuing execution.")
+      return true
+    }
+    println("Workflow is publishing. Waiting...")
+    return false
+  }
+  | last()
+  | map{ event ->
+      // Signal to interval channel to stop generating events.
+      has_published.compareAndSet(false, true)
+      return event[0]
+  }
+  | map {id, state ->
+      println("Creating transfer_complete.txt file.")
+      def complete_file = file("${params.publish_dir}/${state.prefix}/transfer_completed.txt")
+      complete_file.text = "" // This will create a file when it does not exist.
+      [id, state]
+  }
+  | setState(["fastq_output"])
+
+
   emit:
-    output_ch
+    await_ch
 }
 
 def get_version(input) {
diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
index a89f08f..c44de88 100644
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -160,9 +160,9 @@ build_info:
   output: "target/executable/io/interop_summary_to_csv"
   executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
index 549d820..1fb1712 100755
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -454,9 +454,9 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2025-08-05T10:55:23Z"
+LABEL org.opencontainers.image.created="2025-08-08T14:01:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+LABEL org.opencontainers.image.revision="45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index cb85b92..c64bda3 100644
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index 8bee7da..84095ce 100755
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2025-08-05T10:55:23Z"
+LABEL org.opencontainers.image.created="2025-08-08T14:01:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+LABEL org.opencontainers.image.revision="45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index cabf8c0..1efe2b5 100644
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -159,9 +159,9 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index bab2a13..fd96d8f 100755
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2025-08-05T10:55:23Z"
+LABEL org.opencontainers.image.created="2025-08-08T14:01:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+LABEL org.opencontainers.image.revision="45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index 5dd7843..4eb2a2c 100644
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -168,9 +168,9 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index 60c6c94..9aa4f8a 100644
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -3235,9 +3235,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
index cb6dae6..8bba4d4 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -159,9 +159,9 @@ build_info:
   output: "target/nextflow/dataflow/gather_fastqs_and_validate"
   executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index e221cbf..3a86f80 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -3232,9 +3232,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index 4085773..2b98e93 100644
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -268,9 +268,9 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index 1280069..86a995c 100644
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3380,9 +3380,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/detect_demultiplexer/.config.vsh.yaml b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
index 12941ab..d6590c1 100644
--- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml
+++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
@@ -168,9 +168,9 @@ build_info:
   output: "target/nextflow/detect_demultiplexer"
   executable: "target/nextflow/detect_demultiplexer/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/nextflow/detect_demultiplexer/main.nf b/target/nextflow/detect_demultiplexer/main.nf
index c8f7fa8..de8844e 100644
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -3224,9 +3224,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/detect_demultiplexer",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
index d32529d..cb3093c 100644
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -160,9 +160,9 @@ build_info:
   output: "target/nextflow/io/interop_summary_to_csv"
   executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index 2a8793d..b300bf0 100644
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -3233,9 +3233,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index 733ba84..15a0ec3 100644
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index f3e07dc..05290ec 100644
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3302,9 +3302,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index f404e88..774b511 100644
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -159,9 +159,9 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
 package_config:
   name: "demultiplex"
   version: "main"
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 8487fa9..166c271 100644
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -3232,9 +3232,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml
index 2fb2360..117dcc9 100644
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -214,9 +214,9 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805"
+  git_commit: "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-37-g0d4c458"
+  git_tag: "v0.1.1-38-g45cd694"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index cd372f4..413186a 100644
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3296,9 +3296,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "0d4c4584f0d18ab18c21e7d71c43b8deed2c4805",
+    "git_commit" : "45cd6947ef96ae0dd6c38c0e9a791797d68bf4ae",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-37-g0d4c458"
+    "git_tag" : "v0.1.1-38-g45cd694"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3344,11 +3344,17 @@ include { publish } from "${meta.resources_dir}/../../nextflow/io/publish/main.n
 
 // inner workflow
 // user-provided Nextflow code
-def date = new Date().format('yyyyMMdd_hhmmss')
+import java.util.concurrent.ThreadPoolExecutor
+import java.util.concurrent.atomic.AtomicBoolean
 
+def date = new Date().format('yyyyMMdd_hhmmss')
 def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
+session = nextflow.Nextflow.getSession()
+final service = session.publishDirExecutorService()
+
+
 workflow run_wf {
   take:
     input_ch
@@ -3397,13 +3403,16 @@ workflow run_wf {
           state + result + [ to_return: result ]
         },
       )
-      | publish.run(
-        fromState: { id, state ->
-          println(state.plain_output)
+      | map {id, state ->
           def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
           def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"
-
           def prefix = (id2 == "run") ? "" : "${id2}/"
+          def new_state = state + ["prefix": prefix]
+          [id, new_state]
+      }
+      | publish.run(
+        fromState: { id, state ->
+          def prefix = state.prefix
           // These output names are determined by arguments.
           def fastq_output_1 = "${prefix}${state.fastq_output_workflow}"
           def sample_qc_output_1 = "${prefix}${state.sample_qc_output_workflow}"
@@ -3413,18 +3422,6 @@ workflow run_wf {
           def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
 
           println("Publising to ${params.publish_dir}/${prefix}")
-
-          // Create a file to indicate that the publishing (transfer) of files has been completed.
-          // Multiple items can be added to onCompleteActions; which is required when processing multiple sequencing runs at a time.
-          // Alternatively setOnComplete could be used to add actions, but that only adds them at the end of the list (which is executed in order).
-          // The 'completed.txt' file must be created before the onComplete of the integration tests are run, so we need to prepend to the list.
-          workflow.onCompleteActions.add(0, {
-            if (workflow.exitStatus == 0) { 
-              def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt")
-              complete_file.text = "" // This will create a file when it does not exist.
-            }
-          })
-
           [
             input: state.output,
             input_sample_qc: state.output_sample_qc,
@@ -3438,7 +3435,7 @@ workflow run_wf {
             output_demultiplexer_logs: demultiplexer_logs_output,
           ]
         },
-        toState: { id, result, state -> [ fastq_output: state.to_return.output ] },
+        toState: { id, result, state -> [ "fastq_output": state.to_return.output, "prefix": state.prefix ] },
         directives: [
           publishDir: [
             path: "${params.publish_dir}", 
@@ -3448,8 +3445,60 @@ workflow run_wf {
         ]
       )
 
+has_published = new AtomicBoolean(false)
+
+interval_ch = channel.interval('10s'){ i ->
+  // Allow this channel to stop generating events based on a later signal
+  if (has_published.get()) {
+    return channel.STOP
+  }
+  i
+}
+
+await_ch = output_ch
+  // Wait for demultiplexing processes to be done
+  | toSortedList()
+  // Create periodic events in order to check for the publishing to be done
+  | combine(interval_ch)
+  | until { event ->
+    println("Checking if publishing has finished in service ${service}")
+    def running_tasks = null
+    if(service instanceof ThreadPoolExecutor) {
+      def completed_tasks = service.getCompletedTaskCount()
+      def task_count = service.getTaskCount()
+      running_tasks = completed_tasks - task_count
+    }
+    else if( System.getenv('NXF_ENABLE_VIRTUAL_THREADS') ) {
+      running_tasks = service.threadCount()
+    }
+    else {
+      error("Publishing service of class ${service.getClass()} is not supported.")
+    }
+    
+    if (running_tasks == 0) {
+      println("Publishing has finished all current tasks. Continuing execution.")
+      return true
+    }
+    println("Workflow is publishing. Waiting...")
+    return false
+  }
+  | last()
+  | map{ event ->
+      // Signal to interval channel to stop generating events.
+      has_published.compareAndSet(false, true)
+      return event[0]
+  }
+  | map {id, state ->
+      println("Creating transfer_complete.txt file.")
+      def complete_file = file("${params.publish_dir}/${state.prefix}/transfer_completed.txt")
+      complete_file.text = "" // This will create a file when it does not exist.
+      [id, state]
+  }
+  | setState(["fastq_output"])
+
+
   emit:
-    output_ch
+    await_ch
 }
 
 def get_version(input) {