Build branch demultiplex/v0.6 with version v0.6.1 to demultiplex on branch v0.6 (edbd04b)

Build pipeline: viash-hub.demultiplex.v0.6-mrtf2 Source commit: edbd04b6b1 Source message: Bump version to v0.6.1
2025-10-03 14:05:09 +00:00
61 changed files with 221 additions and 210 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,12 @@
+# demultiplex v0.6.1
+
+## Minor changes
+
+* Disable native `bases2fastq` MultiQC report because the workflow generates one itself (PR #66).
+
+* Bump biobox to `v0.4.1`. This updates `bases2fastq` to version `2.2.1` (PR #67).
+
+
 # demultiplex v0.6.0

 # New functionality
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -106,7 +106,7 @@ repositories:
  - name: bb
    type: vsh
    repo: biobox
-    tag: v0.4.0
+    tag: v0.4.1

 runners:
  - type: nextflow
--- a/src/demultiplex/main.nf
+++ b/src/demultiplex/main.nf
@@ -89,6 +89,7 @@ workflow run_wf {
          //"split_lanes": true,
          "legacy_fastq": true, // Illumina style output names
          "group_fastq": true, // No subdir per sample
+          "skip_multi_qc": true // This pipeline generates its own MultiQC report
        ],
        toState: {id, result, state -> 
          def toAdd = [
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "bases2fastq"
-version: "v0.4.0"
+version: "v0.4.1"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -432,9 +432,9 @@ runners:
 engines:
 - type: "docker"
  id: "docker"
-  image: "elembio/bases2fastq:2.2"
+  image: "elembio/bases2fastq:2.2.1"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.0"
+  target_tag: "v0.4.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -452,11 +452,11 @@ build_info:
  output: "target/nextflow/bases2fastq"
  executable: "target/nextflow/bases2fastq/main.nf"
  viash_version: "0.9.4"
-  git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262"
+  git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.4.0"
+  version: "v0.4.1"
  summary: "A curated collection of high-quality, standalone bioinformatics components\
    \ built with [Viash](https://viash.io).\n"
  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
@@ -477,7 +477,7 @@ package_config:
  - ".requirements.commands += ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf
@@ -1,4 +1,4 @@
-// bases2fastq v0.4.0
+// bases2fastq v0.4.1
 // 
 // 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
@@ -3034,7 +3034,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "bases2fastq",
-  "version" : "v0.4.0",
+  "version" : "v0.4.1",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3545,9 +3545,9 @@ meta = [
    {
      "type" : "docker",
      "id" : "docker",
-      "image" : "elembio/bases2fastq:2.2",
+      "image" : "elembio/bases2fastq:2.2.1",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.0",
+      "target_tag" : "v0.4.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3569,12 +3569,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/bases2fastq",
    "viash_version" : "0.9.4",
-    "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262",
+    "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.4.0",
+    "version" : "v0.4.1",
    "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n",
    "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation for components and parameters.\n    * Full exposure of underlying tool arguments.\n    * Containerized (Docker) for dependency management and reproducibility.\n    * Unit tested for verified functionality.\n",
    "viash_version" : "0.9.4",
@@ -3584,7 +3584,7 @@ meta = [
      ".requirements.commands += ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4186,7 +4186,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/bases2fastq",
-    "tag" : "v0.4.0"
+    "tag" : "v0.4.1"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'bases2fastq'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.0'
+  version = 'v0.4.1'
  description = 'Bases2Fastq demultiplexes sequencing data generated by Element Biosciences instruments and converts base calls into FASTQ files.\n'
  author = 'Dries Schaumont'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow_schema.json
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "bcl_convert"
-version: "v0.4.0"
+version: "v0.4.1"
 authors:
 - name: "Toni Verbeiren"
  roles:
@@ -399,7 +399,7 @@ engines:
  id: "docker"
  image: "debian:trixie-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.0"
+  target_tag: "v0.4.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -431,11 +431,11 @@ build_info:
  output: "target/nextflow/bcl_convert"
  executable: "target/nextflow/bcl_convert/main.nf"
  viash_version: "0.9.4"
-  git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262"
+  git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.4.0"
+  version: "v0.4.1"
  summary: "A curated collection of high-quality, standalone bioinformatics components\
    \ built with [Viash](https://viash.io).\n"
  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
@@ -456,7 +456,7 @@ package_config:
  - ".requirements.commands += ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf
@@ -1,4 +1,4 @@
-// bcl_convert v0.4.0
+// bcl_convert v0.4.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "bcl_convert",
-  "version" : "v0.4.0",
+  "version" : "v0.4.1",
  "authors" : [
    {
      "name" : "Toni Verbeiren",
@@ -3531,7 +3531,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:trixie-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.0",
+      "target_tag" : "v0.4.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3571,12 +3571,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/bcl_convert",
    "viash_version" : "0.9.4",
-    "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262",
+    "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.4.0",
+    "version" : "v0.4.1",
    "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n",
    "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation for components and parameters.\n    * Full exposure of underlying tool arguments.\n    * Containerized (Docker) for dependency management and reproducibility.\n    * Unit tested for verified functionality.\n",
    "viash_version" : "0.9.4",
@@ -3586,7 +3586,7 @@ meta = [
      ".requirements.commands += ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4084,7 +4084,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/bcl_convert",
-    "tag" : "v0.4.0"
+    "tag" : "v0.4.1"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'bcl_convert'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.0'
+  version = 'v0.4.1'
  description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n'
  author = 'Toni Verbeiren, Dorien Roosen'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow_schema.json
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "fastqc"
-version: "v0.4.0"
+version: "v0.4.1"
 authors:
 - name: "Theodoro Gasperin Terra Camargo"
  roles:
@@ -334,7 +334,7 @@ engines:
  id: "docker"
  image: "biocontainers/fastqc:v0.11.9_cv8"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.0"
+  target_tag: "v0.4.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -351,11 +351,11 @@ build_info:
  output: "target/nextflow/fastqc"
  executable: "target/nextflow/fastqc/main.nf"
  viash_version: "0.9.4"
-  git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262"
+  git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.4.0"
+  version: "v0.4.1"
  summary: "A curated collection of high-quality, standalone bioinformatics components\
    \ built with [Viash](https://viash.io).\n"
  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
@@ -376,7 +376,7 @@ package_config:
  - ".requirements.commands += ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf
@@ -1,4 +1,4 @@
-// fastqc v0.4.0
+// fastqc v0.4.1
 // 
 // 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
@@ -3034,7 +3034,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "fastqc",
-  "version" : "v0.4.0",
+  "version" : "v0.4.1",
  "authors" : [
    {
      "name" : "Theodoro Gasperin Terra Camargo",
@@ -3397,7 +3397,7 @@ meta = [
      "id" : "docker",
      "image" : "biocontainers/fastqc:v0.11.9_cv8",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.0",
+      "target_tag" : "v0.4.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3419,12 +3419,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/fastqc",
    "viash_version" : "0.9.4",
-    "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262",
+    "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.4.0",
+    "version" : "v0.4.1",
    "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n",
    "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation for components and parameters.\n    * Full exposure of underlying tool arguments.\n    * Containerized (Docker) for dependency management and reproducibility.\n    * Unit tested for verified functionality.\n",
    "viash_version" : "0.9.4",
@@ -3434,7 +3434,7 @@ meta = [
      ".requirements.commands += ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3989,7 +3989,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/fastqc",
-    "tag" : "v0.4.0"
+    "tag" : "v0.4.1"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'fastqc'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.0'
+  version = 'v0.4.1'
  description = 'FastQC - A high throughput sequence QC analysis tool.'
  author = 'Theodoro Gasperin Terra Camargo'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow_schema.json
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "multiqc"
-version: "v0.4.0"
+version: "v0.4.1"
 authors:
 - name: "Dorien Roosen"
  roles:
@@ -436,7 +436,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.4.0"
+  target_tag: "v0.4.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -459,11 +459,11 @@ build_info:
  output: "target/nextflow/multiqc"
  executable: "target/nextflow/multiqc/main.nf"
  viash_version: "0.9.4"
-  git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262"
+  git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.4.0"
+  version: "v0.4.1"
  summary: "A curated collection of high-quality, standalone bioinformatics components\
    \ built with [Viash](https://viash.io).\n"
  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
@@ -484,7 +484,7 @@ package_config:
  - ".requirements.commands += ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf
@@ -1,4 +1,4 @@
-// multiqc v0.4.0
+// multiqc v0.4.1
 // 
 // 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
@@ -3034,7 +3034,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "multiqc",
-  "version" : "v0.4.0",
+  "version" : "v0.4.1",
  "authors" : [
    {
      "name" : "Dorien Roosen",
@@ -3565,7 +3565,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.4.0",
+      "target_tag" : "v0.4.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3596,12 +3596,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/multiqc",
    "viash_version" : "0.9.4",
-    "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262",
+    "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.4.0",
+    "version" : "v0.4.1",
    "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n",
    "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation for components and parameters.\n    * Full exposure of underlying tool arguments.\n    * Containerized (Docker) for dependency management and reproducibility.\n    * Unit tested for verified functionality.\n",
    "viash_version" : "0.9.4",
@@ -3611,7 +3611,7 @@ meta = [
      ".requirements.commands += ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4213,7 +4213,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/multiqc",
-    "tag" : "v0.4.0"
+    "tag" : "v0.4.1"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'multiqc'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.4.0'
+  version = 'v0.4.1'
  description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
  author = 'Dorien Roosen'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow_schema.json
--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "v0.6.0"
+  target_tag: "v0.6.1"
  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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- 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: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- 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 v0.6.0
+# interop_summary_to_csv v0.6.1
 # 
 # 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="2025-09-17T14:02:47Z"
+LABEL org.opencontainers.image.created="2025-10-03T13:21:51Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="b9fa5488ac04b1add4b31c986060979a58aa1a78"
-LABEL org.opencontainers.image.version="v0.6.0"
+LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+LABEL org.opencontainers.image.version="v0.6.1"

 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 v0.6.0"
+  echo "interop_summary_to_csv v0.6.1"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.6.0"
+            echo "interop_summary_to_csv v0.6.1"
            exit
            ;;
        --input)
@@ -759,7 +759,7 @@ if [[ "$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:v0.6.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.1'
  fi

  # print dockerfile
--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "v0.6.0"
+  target_tag: "v0.6.1"
  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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish/_viash.yaml
+++ b/target/executable/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish v0.6.0
+# publish v0.6.1
 # 
 # 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="2025-09-17T14:02:47Z"
+LABEL org.opencontainers.image.created="2025-10-03T13:21:51Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="b9fa5488ac04b1add4b31c986060979a58aa1a78"
-LABEL org.opencontainers.image.version="v0.6.0"
+LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+LABEL org.opencontainers.image.version="v0.6.1"

 VIASHDOCKER
  fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.6.0"
+  echo "publish v0.6.1"
  echo ""
  echo "Publish the processed results of the run"
  echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish v0.6.0"
+            echo "publish v0.6.1"
            exit
            ;;
        --input)
@@ -869,7 +869,7 @@ if [[ "$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:v0.6.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.1'
  fi

  # print dockerfile
--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "v0.6.0"
+  target_tag: "v0.6.1"
  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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/_viash.yaml
+++ b/target/executable/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# untar v0.6.0
+# untar v0.6.1
 # 
 # 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="2025-09-17T14:02:47Z"
+LABEL org.opencontainers.image.created="2025-10-03T13:21:52Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="b9fa5488ac04b1add4b31c986060979a58aa1a78"
-LABEL org.opencontainers.image.version="v0.6.0"
+LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+LABEL org.opencontainers.image.version="v0.6.1"

 VIASHDOCKER
  fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.6.0"
+  echo "untar v0.6.1"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.6.0"
+            echo "untar v0.6.1"
            exit
            ;;
        --input)
@@ -771,7 +771,7 @@ if [[ "$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:v0.6.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.1'
  fi

  # print dockerfile
--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/_viash.yaml
+++ b/target/nextflow/dataflow/combine_samples/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.6.0
+// combine_samples v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "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" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "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 := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }

--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- 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: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- 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 v0.6.0
+// gather_fastqs_and_validate v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "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" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "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 := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }

--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.6.0"
+version: "v0.6.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -165,22 +165,22 @@ dependencies:
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.4.0"
+    tag: "v0.4.1"
 - name: "bases2fastq"
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.4.0"
+    tag: "v0.4.1"
 - name: "fastqc"
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.4.0"
+    tag: "v0.4.1"
 - name: "multiqc"
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.4.0"
+    tag: "v0.4.1"
 - name: "detect_demultiplexer"
  repository:
    type: "local"
@@ -188,7 +188,7 @@ repositories:
 - type: "vsh"
  name: "bb"
  repo: "biobox"
-  tag: "v0.4.0"
+  tag: "v0.4.1"
 license: "MIT"
 links:
  repository: "https://github.com/viash-hub/demultiplex"
@@ -268,21 +268,21 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.4"
-  git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
  - "target/nextflow/io/interop_summary_to_csv"
  - "target/nextflow/dataflow/combine_samples"
-  - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert"
-  - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq"
-  - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc"
-  - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc"
+  - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert"
+  - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq"
+  - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc"
+  - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc"
  - "target/nextflow/detect_demultiplexer"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/demultiplex/_viash.yaml
+++ b/target/nextflow/demultiplex/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.6.0
+// demultiplex v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3246,7 +3246,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.4.0"
+        "tag" : "v0.4.1"
      }
    },
    {
@@ -3254,7 +3254,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.4.0"
+        "tag" : "v0.4.1"
      }
    },
    {
@@ -3262,7 +3262,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.4.0"
+        "tag" : "v0.4.1"
      }
    },
    {
@@ -3270,7 +3270,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.4.0"
+        "tag" : "v0.4.1"
      }
    },
    {
@@ -3285,7 +3285,7 @@ meta = [
      "type" : "vsh",
      "name" : "bb",
      "repo" : "biobox",
-      "tag" : "v0.4.0"
+      "tag" : "v0.4.1"
    }
  ],
  "license" : "MIT",
@@ -3380,12 +3380,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3402,7 +3402,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3426,10 +3426,10 @@ include { untar } from "${meta.resources_dir}/../../nextflow/io/untar/main.nf"
 include { gather_fastqs_and_validate } from "${meta.resources_dir}/../../nextflow/dataflow/gather_fastqs_and_validate/main.nf"
 include { interop_summary_to_csv } from "${meta.resources_dir}/../../nextflow/io/interop_summary_to_csv/main.nf"
 include { combine_samples } from "${meta.resources_dir}/../../nextflow/dataflow/combine_samples/main.nf"
-include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/main.nf"
-include { bases2fastq } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/main.nf"
-include { fastqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/main.nf"
-include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/main.nf"
+include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf"
+include { bases2fastq } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf"
+include { fastqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf"
+include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf"
 include { detect_demultiplexer } from "${meta.resources_dir}/../../nextflow/detect_demultiplexer/main.nf"

 // inner workflow
@@ -3525,6 +3525,7 @@ workflow run_wf {
          //"split_lanes": true,
          "legacy_fastq": true, // Illumina style output names
          "group_fastq": true, // No subdir per sample
+          "skip_multi_qc": true // This pipeline generates its own MultiQC report
        ],
        toState: {id, result, state -> 
          def toAdd = [
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  description = 'Demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml
+++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "detect_demultiplexer"
-version: "v0.6.0"
+version: "v0.6.1"
 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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/detect_demultiplexer/_viash.yaml
+++ b/target/nextflow/detect_demultiplexer/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -1,4 +1,4 @@
-// detect_demultiplexer v0.6.0
+// detect_demultiplexer v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "argument_groups" : [
    {
      "name" : "Arguments",
@@ -3224,12 +3224,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/detect_demultiplexer",
    "viash_version" : "0.9.4",
-    "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "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 := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n'
 }

--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "v0.6.0"
+  target_tag: "v0.6.1"
  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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- 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: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- 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 v0.6.0
+// interop_summary_to_csv v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3203,7 +3203,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.0",
+      "target_tag" : "v0.6.1",
      "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" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3255,7 +3255,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3699,7 +3699,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.6.0"
+    "tag" : "v0.6.1"
  },
  "tag" : "$id"
 }'''),
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
 }

 process.container = 'nextflow/bash:latest'
--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "v0.6.0"
+  target_tag: "v0.6.1"
  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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish/_viash.yaml
+++ b/target/nextflow/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.6.0
+// publish v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3279,7 +3279,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.0",
+      "target_tag" : "v0.6.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3302,12 +3302,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.4",
-    "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3324,7 +3324,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3799,7 +3799,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.6.0"
+    "tag" : "v0.6.1"
  },
  "tag" : "$id"
 }'''),
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  description = 'Publish the processed results of the run'
 }

--- 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: "v0.6.0"
+version: "v0.6.1"
 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: "v0.6.0"
+  target_tag: "v0.6.1"
  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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/_viash.yaml
+++ b/target/nextflow/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.6.0
+// untar v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3209,7 +3209,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.0",
+      "target_tag" : "v0.6.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3232,12 +3232,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.4",
-    "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3254,7 +3254,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3728,7 +3728,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.6.0"
+    "tag" : "v0.6.1"
  },
  "tag" : "$id"
 }'''),
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  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'
 }

--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.6.0"
+version: "v0.6.1"
 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: "b9fa5488ac04b1add4b31c986060979a58aa1a78"
+  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
  git_remote: "https://github.com/viash-hub/demultiplex"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.6.0"
+  version: "v0.6.1"
  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 := 'v0.6.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/runner/_viash.yaml
+++ b/target/nextflow/runner/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.0
+version: v0.6.1
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.6.0
+// runner v0.6.1
 // 
 // 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" : "v0.6.0",
+  "version" : "v0.6.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3301,12 +3301,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78",
+    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.0",
+    "version" : "v0.6.1",
    "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 := 'v0.6.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- 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 = 'v0.6.0'
+  version = 'v0.6.1'
  description = 'Runner for demultiplexing of raw sequencing data'
 }