From 7cc9c95cb166c0479fcde7c114ff86dfdb3371bb Mon Sep 17 00:00:00 2001
From: CI <toni@data-intuitive.com>
Date: Mon, 11 Aug 2025 07:32:55 +0000
Subject: [PATCH] Build branch v0.4 with version v0.4.4 (02d0c0b)

Build pipeline: viash-hub.demultiplex.v0.4-z4www

Source commit: https://github.com/viash-hub/demultiplex/commit/02d0c0b1680935b912292e7cf39ef8a8b4334558

Source message: Bump version to v0.4.4
---
 CHANGELOG.md                                  |  6 ++
 _viash.yaml                                   |  2 +-
 src/runner/main.nf                            | 85 ++++++++++++----
 .../interop_summary_to_csv/.config.vsh.yaml   | 12 +--
 .../io/interop_summary_to_csv/_viash.yaml     |  2 +-
 .../interop_summary_to_csv                    | 14 +--
 target/executable/io/publish/.config.vsh.yaml | 12 +--
 target/executable/io/publish/_viash.yaml      |  2 +-
 target/executable/io/publish/publish          | 14 +--
 target/executable/io/untar/.config.vsh.yaml   | 12 +--
 target/executable/io/untar/_viash.yaml        |  2 +-
 target/executable/io/untar/untar              | 14 +--
 .../dataflow/combine_samples/.config.vsh.yaml | 10 +-
 .../dataflow/combine_samples/_viash.yaml      |  2 +-
 .../nextflow/dataflow/combine_samples/main.nf | 12 +--
 .../dataflow/combine_samples/nextflow.config  |  2 +-
 .../.config.vsh.yaml                          | 10 +-
 .../gather_fastqs_and_validate/_viash.yaml    |  2 +-
 .../gather_fastqs_and_validate/main.nf        | 12 +--
 .../nextflow.config                           |  2 +-
 target/nextflow/demultiplex/.config.vsh.yaml  | 10 +-
 target/nextflow/demultiplex/_viash.yaml       |  2 +-
 target/nextflow/demultiplex/main.nf           | 12 +--
 target/nextflow/demultiplex/nextflow.config   |  2 +-
 .../detect_demultiplexer/.config.vsh.yaml     | 10 +-
 .../nextflow/detect_demultiplexer/_viash.yaml |  2 +-
 target/nextflow/detect_demultiplexer/main.nf  | 12 +--
 .../detect_demultiplexer/nextflow.config      |  2 +-
 .../interop_summary_to_csv/.config.vsh.yaml   | 12 +--
 .../io/interop_summary_to_csv/_viash.yaml     |  2 +-
 .../io/interop_summary_to_csv/main.nf         | 16 +--
 .../io/interop_summary_to_csv/nextflow.config |  2 +-
 target/nextflow/io/publish/.config.vsh.yaml   | 12 +--
 target/nextflow/io/publish/_viash.yaml        |  2 +-
 target/nextflow/io/publish/main.nf            | 16 +--
 target/nextflow/io/publish/nextflow.config    |  2 +-
 target/nextflow/io/untar/.config.vsh.yaml     | 12 +--
 target/nextflow/io/untar/_viash.yaml          |  2 +-
 target/nextflow/io/untar/main.nf              | 16 +--
 target/nextflow/io/untar/nextflow.config      |  2 +-
 target/nextflow/runner/.config.vsh.yaml       | 10 +-
 target/nextflow/runner/_viash.yaml            |  2 +-
 target/nextflow/runner/main.nf                | 97 ++++++++++++++-----
 target/nextflow/runner/nextflow.config        |  2 +-
 44 files changed, 298 insertions(+), 190 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 37c8da9..85b2aa7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# demultiplex v0.4.4
+
+## Bug fixes
+
+* Only add the `transfer_complete.txt` files when the exitcode for the workflow is 0 (PR #58)
+
 # demultiplex v0.4.3
 
 ## Minor changes
diff --git a/_viash.yaml b/_viash.yaml
index cef6a4d..def5c57 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/src/runner/main.nf b/src/runner/main.nf
index 78cba99..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}${state.sample_qc_output_workflow}"
@@ -67,16 +76,6 @@ workflow run_wf {
           def run_information_output_1 = "${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, {
-            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,
@@ -90,7 +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}", 
@@ -100,8 +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 7c895a0..af78d74 100644
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -135,7 +135,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.3"
+  target_tag: "v0.4.4"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,12 +160,12 @@ 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: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -181,7 +181,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/interop_summary_to_csv/_viash.yaml b/target/executable/io/interop_summary_to_csv/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/executable/io/interop_summary_to_csv/_viash.yaml
+++ b/target/executable/io/interop_summary_to_csv/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
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 38a2f78..36b3783 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
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# interop_summary_to_csv v0.4.3
+# interop_summary_to_csv v0.4.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ 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="2025-08-01T13:26:46Z"
+LABEL org.opencontainers.image.created="2025-08-11T07:05:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="aa8803720f098287518db3d2dc74eff24cf003f1"
-LABEL org.opencontainers.image.version="v0.4.3"
+LABEL org.opencontainers.image.revision="02d0c0b1680935b912292e7cf39ef8a8b4334558"
+LABEL org.opencontainers.image.version="v0.4.4"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.4.3"
+  echo "interop_summary_to_csv v0.4.4"
   echo ""
   echo "Input arguments:"
   echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.4.3"
+            echo "interop_summary_to_csv v0.4.4"
             exit
             ;;
         --input)
@@ -759,7 +759,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.4.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.4.4'
   fi
 
   # print dockerfile
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index 1ea90f8..3f3189f 100644
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.3"
+  target_tag: "v0.4.4"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,12 +222,12 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -243,7 +243,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/publish/_viash.yaml b/target/executable/io/publish/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/executable/io/publish/_viash.yaml
+++ b/target/executable/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index 5ec5d61..ead9032 100755
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish v0.4.3
+# publish v0.4.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ 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="2025-08-01T13:26:46Z"
+LABEL org.opencontainers.image.created="2025-08-11T07:05:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="aa8803720f098287518db3d2dc74eff24cf003f1"
-LABEL org.opencontainers.image.version="v0.4.3"
+LABEL org.opencontainers.image.revision="02d0c0b1680935b912292e7cf39ef8a8b4334558"
+LABEL org.opencontainers.image.version="v0.4.4"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.4.3"
+  echo "publish v0.4.4"
   echo ""
   echo "Publish the processed results of the run"
   echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish v0.4.3"
+            echo "publish v0.4.4"
             exit
             ;;
         --input)
@@ -869,7 +869,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.4.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.4.4'
   fi
 
   # print dockerfile
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index 69e8030..d9b2cb6 100644
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.3"
+  target_tag: "v0.4.4"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -159,12 +159,12 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -180,7 +180,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/untar/_viash.yaml b/target/executable/io/untar/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/executable/io/untar/_viash.yaml
+++ b/target/executable/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index 92d43a5..db27c05 100755
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# untar v0.4.3
+# untar v0.4.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ 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="2025-08-01T13:26:46Z"
+LABEL org.opencontainers.image.created="2025-08-11T07:05:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="aa8803720f098287518db3d2dc74eff24cf003f1"
-LABEL org.opencontainers.image.version="v0.4.3"
+LABEL org.opencontainers.image.revision="02d0c0b1680935b912292e7cf39ef8a8b4334558"
+LABEL org.opencontainers.image.version="v0.4.4"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.4.3"
+  echo "untar v0.4.4"
   echo ""
   echo "Unpack a .tar file. When the contents of the .tar file is just a single"
   echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.4.3"
+            echo "untar v0.4.4"
             exit
             ;;
         --input)
@@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.4.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.4.4'
   fi
 
   # print dockerfile
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index c35a48a..e91d2a5 100644
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -168,12 +168,12 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -189,7 +189,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/dataflow/combine_samples/_viash.yaml b/target/nextflow/dataflow/combine_samples/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/dataflow/combine_samples/_viash.yaml
+++ b/target/nextflow/dataflow/combine_samples/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index e351204..4856f78 100644
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.4.3
+// combine_samples v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_samples",
   "namespace" : "dataflow",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3235,13 +3235,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3258,7 +3258,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config
index 65f4256..e922a69 100644
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/combine_samples'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }
 
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 4c33d45..9780a9b 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -159,12 +159,12 @@ 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: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -180,7 +180,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index fd91d4c..147e9d1 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.4.3
+// gather_fastqs_and_validate v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "gather_fastqs_and_validate",
   "namespace" : "dataflow",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3232,13 +3232,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3255,7 +3255,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
index e8fe435..fcc65c0 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/gather_fastqs_and_validate'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }
 
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index b2fbff1..b4a2720 100644
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -268,9 +268,9 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -283,7 +283,7 @@ build_info:
   - "target/nextflow/detect_demultiplexer"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -299,7 +299,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/demultiplex/_viash.yaml b/target/nextflow/demultiplex/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/demultiplex/_viash.yaml
+++ b/target/nextflow/demultiplex/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index 163ea3a..3fbd9c8 100644
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.4.3
+// demultiplex v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "demultiplex",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3380,13 +3380,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3403,7 +3403,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config
index 0a811a3..29ac86a 100644
--- a/target/nextflow/demultiplex/nextflow.config
+++ b/target/nextflow/demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'Demultiplexing of raw sequencing data'
 }
 
diff --git a/target/nextflow/detect_demultiplexer/.config.vsh.yaml b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
index 37a433c..b51ce0a 100644
--- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml
+++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "detect_demultiplexer"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -168,12 +168,12 @@ build_info:
   output: "target/nextflow/detect_demultiplexer"
   executable: "target/nextflow/detect_demultiplexer/main.nf"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -189,7 +189,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/detect_demultiplexer/_viash.yaml b/target/nextflow/detect_demultiplexer/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/detect_demultiplexer/_viash.yaml
+++ b/target/nextflow/detect_demultiplexer/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/detect_demultiplexer/main.nf b/target/nextflow/detect_demultiplexer/main.nf
index aeea363..7e7ee81 100644
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -1,4 +1,4 @@
-// detect_demultiplexer v0.4.3
+// detect_demultiplexer v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "detect_demultiplexer",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3224,13 +3224,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/detect_demultiplexer",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3247,7 +3247,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/detect_demultiplexer/nextflow.config b/target/nextflow/detect_demultiplexer/nextflow.config
index 18b4d3c..e0c39c9 100644
--- a/target/nextflow/detect_demultiplexer/nextflow.config
+++ b/target/nextflow/detect_demultiplexer/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'detect_demultiplexer'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n'
 }
 
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 024c955..5d2504c 100644
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -135,7 +135,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.3"
+  target_tag: "v0.4.4"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,12 +160,12 @@ 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: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -181,7 +181,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/interop_summary_to_csv/_viash.yaml b/target/nextflow/io/interop_summary_to_csv/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/io/interop_summary_to_csv/_viash.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index 3f23621..918a721 100644
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.4.3
+// interop_summary_to_csv v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "interop_summary_to_csv",
   "namespace" : "io",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3203,7 +3203,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.3",
+      "target_tag" : "v0.4.4",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3233,13 +3233,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3256,7 +3256,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3700,7 +3700,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.4.3"
+    "tag" : "v0.4.4"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config
index 3fc1019..9b3b212 100644
--- a/target/nextflow/io/interop_summary_to_csv/nextflow.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'io/interop_summary_to_csv'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
 }
 
 process.container = 'nextflow/bash:latest'
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index 0f2a712..64adc99 100644
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.3"
+  target_tag: "v0.4.4"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,12 +222,12 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -243,7 +243,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/publish/_viash.yaml b/target/nextflow/io/publish/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/io/publish/_viash.yaml
+++ b/target/nextflow/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index ce1dda9..6bce2b9 100644
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.4.3
+// publish v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish",
   "namespace" : "io",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3279,7 +3279,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.3",
+      "target_tag" : "v0.4.4",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3302,13 +3302,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3325,7 +3325,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3800,7 +3800,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.4.3"
+    "tag" : "v0.4.4"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config
index 045ad1f..c5fad5b 100644
--- a/target/nextflow/io/publish/nextflow.config
+++ b/target/nextflow/io/publish/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'Publish the processed results of the run'
 }
 
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index 0cbd6bd..5bae290 100644
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.3"
+  target_tag: "v0.4.4"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -159,12 +159,12 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -180,7 +180,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/untar/_viash.yaml b/target/nextflow/io/untar/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/io/untar/_viash.yaml
+++ b/target/nextflow/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index e7aeff2..45755f3 100644
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.4.3
+// untar v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "untar",
   "namespace" : "io",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3209,7 +3209,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.3",
+      "target_tag" : "v0.4.4",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3232,13 +3232,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3255,7 +3255,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3729,7 +3729,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.4.3"
+    "tag" : "v0.4.4"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config
index 618f0ce..a216da6 100644
--- a/target/nextflow/io/untar/nextflow.config
+++ b/target/nextflow/io/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'io/untar'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }
 
diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml
index 4ff2a70..13ea483 100644
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.4.3"
+version: "v0.4.4"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -214,15 +214,15 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1"
+  git_commit: "02d0c0b1680935b912292e7cf39ef8a8b4334558"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.4.2-2-gaa88037"
+  git_tag: "v0.4.2-5-g02d0c0b"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
 package_config:
   name: "demultiplex"
-  version: "v0.4.3"
+  version: "v0.4.4"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -238,7 +238,7 @@ package_config:
     )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/runner/_viash.yaml b/target/nextflow/runner/_viash.yaml
index 9c24dd5..37dac5c 100644
--- a/target/nextflow/runner/_viash.yaml
+++ b/target/nextflow/runner/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.4.3
+version: v0.4.4
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index b3c7c36..314cb72 100644
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.4.3
+// runner v0.4.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "runner",
-  "version" : "v0.4.3",
+  "version" : "v0.4.4",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3296,13 +3296,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1",
+    "git_commit" : "02d0c0b1680935b912292e7cf39ef8a8b4334558",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.4.2-2-gaa88037"
+    "git_tag" : "v0.4.2-5-g02d0c0b"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.4.3",
+    "version" : "v0.4.4",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3319,7 +3319,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.4'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3344,11 +3344,17 @@ include { publish } from "${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}${state.sample_qc_output_workflow}"
@@ -3413,16 +3422,6 @@ workflow run_wf {
           def run_information_output_1 = "${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, {
-            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,
@@ -3436,7 +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}", 
@@ -3446,8 +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) {
diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config
index 658408a..fa5621d 100644
--- a/target/nextflow/runner/nextflow.config
+++ b/target/nextflow/runner/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'runner'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.3'
+  version = 'v0.4.4'
   description = 'Runner for demultiplexing of raw sequencing data'
 }