diff --git a/CHANGELOG.md b/CHANGELOG.md
index 21a7ab5..42af636 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# demultiplex v0.6.3
+
+## Bug fixes
+
+* `runner`: fix resume functionality when used as subworkflow (PR #70).
+
 # demultiplex v0.6.2
 
 ## Bug fixes
diff --git a/_viash.yaml b/_viash.yaml
index e0d7e07..6edb622 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/src/runner/main.nf b/src/runner/main.nf
index 09495a9..72efffb 100644
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -86,11 +86,16 @@ workflow run_wf {
           ]
         },
         toState: { id, result, state -> [ 
-            "fastq_output": result.output, 
+            // Most of the output is copied from the input state
+            // This allows for resume functionality to work when using any of these outputs
+            // because the restult state contains a unique date in the path.
+            // Only for the sample QC ouput, multiple results are gathered 
+            // so we must use the resulting output directory.
+            "fastq_output": state.output, 
             "prefix": state.prefix,
-            "multiqc_output": result.output_multiqc,
+            "multiqc_output": state.multiqc_output,
             "sample_qc_output": result.output_sample_qc,
-            "demultiplexer_logs": result.output_demultiplexer_logs,
+            "demultiplexer_logs": state.demultiplexer_logs,
           ]
         },
         directives: [
diff --git a/src/runner/test.nf b/src/runner/test.nf
index 40bebb1..7685575 100644
--- a/src/runner/test.nf
+++ b/src/runner/test.nf
@@ -21,7 +21,7 @@ if (!params.publish_dir) {
             println "Failed to delete temp directory: $e"
         }
     }))
-    params.publish_dir = tempDir
+    params.publish_dir = tempDir.toString()
 }
 // The module inherits the parameters defined before the include statement, 
 // therefore any parameters set afterwards will not be used by the module.
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 7260eee..3f6effd 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: "v0.6.2"
+version: "v0.6.3"
 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: "v0.6.2"
+  target_tag: "v0.6.3"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,11 +160,11 @@ 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: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   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 e0d7e07..6edb622 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: v0.6.2
+version: v0.6.3
 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 2c6b9f9..0512f9b 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 v0.6.2
+# interop_summary_to_csv v0.6.3
 # 
 # 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="2025-10-09T09:23:27Z"
+LABEL org.opencontainers.image.created="2025-11-05T08:18:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
-LABEL org.opencontainers.image.version="v0.6.2"
+LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
+LABEL org.opencontainers.image.version="v0.6.3"
 
 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 v0.6.2"
+  echo "interop_summary_to_csv v0.6.3"
   echo ""
   echo "Input arguments:"
   echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.6.2"
+            echo "interop_summary_to_csv v0.6.3"
             exit
             ;;
         --input)
@@ -759,7 +759,7 @@ if [[ "$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:v0.6.2'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.3'
   fi
 
   # print dockerfile
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index e36b207..a6d22ea 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: "v0.6.2"
+version: "v0.6.3"
 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: "v0.6.2"
+  target_tag: "v0.6.3"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,11 +222,11 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -242,7 +242,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/publish/_viash.yaml b/target/executable/io/publish/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/executable/io/publish/_viash.yaml
+++ b/target/executable/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index 1e968b1..7e107d3 100755
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish v0.6.2
+# publish v0.6.3
 # 
 # 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="2025-10-09T09:23:27Z"
+LABEL org.opencontainers.image.created="2025-11-05T08:18:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
-LABEL org.opencontainers.image.version="v0.6.2"
+LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
+LABEL org.opencontainers.image.version="v0.6.3"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.6.2"
+  echo "publish v0.6.3"
   echo ""
   echo "Publish the processed results of the run"
   echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish v0.6.2"
+            echo "publish v0.6.3"
             exit
             ;;
         --input)
@@ -869,7 +869,7 @@ if [[ "$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:v0.6.2'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.3'
   fi
 
   # print dockerfile
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index 86b2ee3..31bcf95 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: "v0.6.2"
+version: "v0.6.3"
 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: "v0.6.2"
+  target_tag: "v0.6.3"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -159,11 +159,11 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -179,7 +179,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/untar/_viash.yaml b/target/executable/io/untar/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/executable/io/untar/_viash.yaml
+++ b/target/executable/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index c72e36b..292f6a4 100755
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# untar v0.6.2
+# untar v0.6.3
 # 
 # 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="2025-10-09T09:23:27Z"
+LABEL org.opencontainers.image.created="2025-11-05T08:18:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
-LABEL org.opencontainers.image.version="v0.6.2"
+LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
+LABEL org.opencontainers.image.version="v0.6.3"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.6.2"
+  echo "untar v0.6.3"
   echo ""
   echo "Unpack a .tar file. When the contents of the .tar file is just a single"
   echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.6.2"
+            echo "untar v0.6.3"
             exit
             ;;
         --input)
@@ -771,7 +771,7 @@ if [[ "$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:v0.6.2'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.3'
   fi
 
   # print dockerfile
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index 4e2a07b..75c522d 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: "v0.6.2"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -168,11 +168,11 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -188,7 +188,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/dataflow/combine_samples/_viash.yaml b/target/nextflow/dataflow/combine_samples/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/nextflow/dataflow/combine_samples/_viash.yaml
+++ b/target/nextflow/dataflow/combine_samples/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index fddbe71..b850bea 100644
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.6.2
+// combine_samples v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3235,12 +3235,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3257,7 +3257,7 @@ 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 := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config
index 9601519..7184de1 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 = 'v0.6.2'
+  version = 'v0.6.3'
   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 9fae50e..069db71 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: "v0.6.2"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -159,11 +159,11 @@ 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: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -179,7 +179,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   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 e0d7e07..6edb622 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: v0.6.2
+version: v0.6.3
 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 2e8cfd7..19c7085 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 v0.6.2
+// gather_fastqs_and_validate v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3232,12 +3232,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3254,7 +3254,7 @@ 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 := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "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 31d12fd..2751e80 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 = 'v0.6.2'
+  version = 'v0.6.3'
   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 68d9fd0..ff7331b 100644
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.6.2"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -268,7 +268,7 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
   dependencies:
   - "target/nextflow/io/untar"
@@ -282,7 +282,7 @@ build_info:
   - "target/nextflow/detect_demultiplexer"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -298,7 +298,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/demultiplex/_viash.yaml b/target/nextflow/demultiplex/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/nextflow/demultiplex/_viash.yaml
+++ b/target/nextflow/demultiplex/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index 490814e..19456fd 100644
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.6.2
+// demultiplex v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3380,12 +3380,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3402,7 +3402,7 @@ 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 := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config
index 083c14a..5aef8c2 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 = 'v0.6.2'
+  version = 'v0.6.3'
   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 6ade41e..c179cc4 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: "v0.6.2"
+version: "v0.6.3"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -168,11 +168,11 @@ build_info:
   output: "target/nextflow/detect_demultiplexer"
   executable: "target/nextflow/detect_demultiplexer/main.nf"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -188,7 +188,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/detect_demultiplexer/_viash.yaml b/target/nextflow/detect_demultiplexer/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/nextflow/detect_demultiplexer/_viash.yaml
+++ b/target/nextflow/detect_demultiplexer/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/detect_demultiplexer/main.nf b/target/nextflow/detect_demultiplexer/main.nf
index a1dd570..37cebc4 100644
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -1,4 +1,4 @@
-// detect_demultiplexer v0.6.2
+// detect_demultiplexer v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3224,12 +3224,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/detect_demultiplexer",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3246,7 +3246,7 @@ 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 := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/detect_demultiplexer/nextflow.config b/target/nextflow/detect_demultiplexer/nextflow.config
index de78032..bdb032a 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 = 'v0.6.2'
+  version = 'v0.6.3'
   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 72299a6..6341de2 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: "v0.6.2"
+version: "v0.6.3"
 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: "v0.6.2"
+  target_tag: "v0.6.3"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,11 +160,11 @@ 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: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   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 e0d7e07..6edb622 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: v0.6.2
+version: v0.6.3
 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 284d161..d7d5c1d 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 v0.6.2
+// interop_summary_to_csv v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3203,7 +3203,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.2",
+      "target_tag" : "v0.6.3",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3233,12 +3233,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3255,7 +3255,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3699,7 +3699,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.6.2"
+    "tag" : "v0.6.3"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config
index 8b70408..cb1d4a4 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 = 'v0.6.2'
+  version = 'v0.6.3'
 }
 
 process.container = 'nextflow/bash:latest'
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index 991e4dc..27124bb 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: "v0.6.2"
+version: "v0.6.3"
 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: "v0.6.2"
+  target_tag: "v0.6.3"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,11 +222,11 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -242,7 +242,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/publish/_viash.yaml b/target/nextflow/io/publish/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/nextflow/io/publish/_viash.yaml
+++ b/target/nextflow/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index 2ba92a0..f5a6609 100644
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.6.2
+// publish v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3279,7 +3279,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.2",
+      "target_tag" : "v0.6.3",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3302,12 +3302,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3324,7 +3324,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3799,7 +3799,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.6.2"
+    "tag" : "v0.6.3"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config
index 45b814b..1d1e24e 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 = 'v0.6.2'
+  version = 'v0.6.3'
   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 ac5d882..69091de 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: "v0.6.2"
+version: "v0.6.3"
 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: "v0.6.2"
+  target_tag: "v0.6.3"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -159,11 +159,11 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -179,7 +179,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/untar/_viash.yaml b/target/nextflow/io/untar/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/nextflow/io/untar/_viash.yaml
+++ b/target/nextflow/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 5cd82cb..ae283e6 100644
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.6.2
+// untar v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3209,7 +3209,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.2",
+      "target_tag" : "v0.6.3",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3232,12 +3232,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3254,7 +3254,7 @@ meta = [
       ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3728,7 +3728,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.6.2"
+    "tag" : "v0.6.3"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config
index d0c3a18..4d0ac28 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 = 'v0.6.2'
+  version = 'v0.6.3'
   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 de83ad3..0cba0b8 100644
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.6.2"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -217,14 +217,14 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
   git_remote: "https://github.com/viash-hub/demultiplex"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
 package_config:
   name: "demultiplex"
-  version: "v0.6.2"
+  version: "v0.6.3"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -240,7 +240,7 @@ 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 := 'v0.6.2'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/runner/_viash.yaml b/target/nextflow/runner/_viash.yaml
index e0d7e07..6edb622 100644
--- a/target/nextflow/runner/_viash.yaml
+++ b/target/nextflow/runner/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.2
+version: v0.6.3
 description: |
   Demultiplexing pipeline
 license: MIT
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index b2e3ff1..e6894e9 100644
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.6.2
+// runner v0.6.3
 // 
 // 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" : "v0.6.2",
+  "version" : "v0.6.3",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3301,12 +3301,12 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "16ba5d4283de8cd430a5e8ae9b1d8ceeecaa813a",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.6.2",
+    "version" : "v0.6.3",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3323,7 +3323,7 @@ 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 := 'v0.6.2'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3436,11 +3436,16 @@ workflow run_wf {
           ]
         },
         toState: { id, result, state -> [ 
-            "fastq_output": result.output, 
+            // Most of the output is copied from the input state
+            // This allows for resume functionality to work when using any of these outputs
+            // because the restult state contains a unique date in the path.
+            // Only for the sample QC ouput, multiple results are gathered 
+            // so we must use the resulting output directory.
+            "fastq_output": state.output, 
             "prefix": state.prefix,
-            "multiqc_output": result.output_multiqc,
+            "multiqc_output": state.multiqc_output,
             "sample_qc_output": result.output_sample_qc,
-            "demultiplexer_logs": result.output_demultiplexer_logs,
+            "demultiplexer_logs": state.demultiplexer_logs,
           ]
         },
         directives: [
diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config
index 3537935..d3d56e2 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 = 'v0.6.2'
+  version = 'v0.6.3'
   description = 'Runner for demultiplexing of raw sequencing data'
 }