Build branch htrnaseq/v0.14 with version v0.14.7 to htrnaseq on branch v0.14 (07ba686)

Build pipeline: viash-hub.htrnaseq.v0.14.7-lr47z Source commit: 07ba686a46 Source message: Bump version to v0.14.7
2026-04-02 14:08:44 +00:00
parent 44dc2ea48d
commit 8bc82c81e3
130 changed files with 729 additions and 608 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# htrnaseq v0.14.7
+
+## Bug fixes
+
+* Revert breaking changes from PR #95 and re-implement writing (sub-)workflow version to a separate file (PR #103).
+
 # htrnaseq v0.14.6

 ## Minor changes
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/src/io/publish_results/code.sh
+++ b/src/io/publish_results/code.sh
@@ -19,6 +19,7 @@ declare -A path_pars_dirs=(
 declare -A path_pars_files=(
  ["par_html_report_output"]="par_html_report"
  ["par_run_params_output"]="par_run_params"
+  ["par_run_metadata_output"]="par_run_metadata"
 )

 echo "Canonicalizing output paths."
--- a/src/io/publish_results/config.vsh.yaml
+++ b/src/io/publish_results/config.vsh.yaml
@@ -35,6 +35,9 @@ argument_groups:
      - name: "--run_params"
        type: file
        required: true
+      - name: "--run_metadata"
+        type: file
+        required: true
  - name: Output directory
    description: |
      Determines the name of output directories
@@ -69,6 +72,9 @@ argument_groups:
      - name: "--run_params_output"
        type: file
        direction: output
+      - name: "--run_metadata_output"
+        type: file
+        direction: output
      - name: "--html_report_output"
        type: file
        direction: output
--- a/src/utils/save_params/config.vsh.yaml
+++ b/src/utils/save_params/config.vsh.yaml
@@ -16,11 +16,6 @@ argument_groups:
          base64 encoded yaml containing the state
        type: string
        required: true
-      - name: "--workflow_analysis"
-        description: |
-          Base64 encoded YAML containing workflow analysis information (name and version for all workflows)
-        type: string
-        required: false
    
  - name: Outputs
    arguments:
@@ -28,9 +23,9 @@ argument_groups:
        description: |
          The output YAML file
        type: file
-        default: "params.yaml"
        direction: output
        required: true
+        example: "output.yaml"

 resources:
  - type: python_script
--- a/src/utils/save_params/script.py
+++ b/src/utils/save_params/script.py
@@ -6,23 +6,14 @@ import base64
 par = {
    "id": "sample_one",
    "params_yaml": "cGFyYW1zX3lhbWw6IHt9Cg==",
-    "workflow_analysis": "LSBuYW1lOiBhbm5vdFZpc1FDX3dmCiAgdmVyc2lvbjogMC4xLjAK",
    "output": "output.yaml"
 }
 ## VIASH END

-# Custom representer to preserve dict order in YAML output
-# Note: Python 3.7+ dicts maintain insertion order by default
-def represent_dict(dumper, data):
-    return dumper.represent_dict(data.items())
-
 class Dumper(yaml.Dumper):
    def increase_indent(self, flow=False, indentless=False):
        return super(Dumper, self).increase_indent(flow, False)

-# Register the representer for dicts to preserve order
-Dumper.add_representer(dict, represent_dict)
-
 def decode_params_yaml(encoded_yaml):
    yaml_bytes = base64.b64decode(encoded_yaml)
    yaml_string = yaml_bytes.decode('utf-8')
@@ -32,24 +23,6 @@ def decode_params_yaml(encoded_yaml):

 params = decode_params_yaml(par['params_yaml'])

-# Build the output structure
-output_data = params  # params is a list of states
-
-# Add workflow analysis information if provided
-if par.get('workflow_analysis'):
-    try:
-        analysis_bytes = base64.b64decode(par['workflow_analysis'])
-        analysis_string = analysis_bytes.decode('utf-8')
-        analysis = yaml.safe_load(analysis_string)
-        # Since params is a list, create a dict wrapper
-        output_data = {
-            'params': params,
-            'analysis': analysis
-        }
-    except (TypeError, ValueError) as e:
-        e.add_note("Could not parse workflow_analysis YAML.")
-        raise
-
 with open(par["output"], 'w') as f:
-    yaml.dump(output_data, f, default_flow_style=False, Dumper=Dumper)
+    yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)

--- a/src/workflows/runner/config.vsh.yaml
+++ b/src/workflows/runner/config.vsh.yaml
@@ -73,6 +73,12 @@ argument_groups:
        type: file
        direction: output
        default: params.yaml
+      - name: "--run_metadata"
+        type: file
+        description: |
+          YAML file containing meta information about the file — .e.g. versions of (sub)-workflows.
+        direction: output
+        default: metadata.yaml
      - name: "--star_output_dir"
        type: file
        direction: output
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -36,17 +36,20 @@ def get_workflow_analysis() {
  }
  
  // Build main analysis entry with dependencies using LinkedHashMap for order
-  def main_entry = new LinkedHashMap()
-  main_entry.name = meta.config.name ?: "unknown_name"
-  main_entry.version = meta.config.version ?: "unknown_version"
-  main_entry.dependencies = dependencies
+  def main_entry = [
+    "name": meta.config.name ?: "unknown_name",
+    "version": meta.config.version ?: "unknown_version",
+    "dependencies": dependencies
+  ]
  
-  def analysis = [main_entry]
+  def analysis = ["versions": [main_entry]]
  
  println("Analysis workflows: ${analysis}")
  return analysis
 }

+
+
 /* 
 This is a utility workflow that gathers the input events and saves their state to a YAML file.
 */
@@ -63,12 +66,21 @@ workflow save_params_wf {
        def all_states = states.collect{it[1]}
        def run_params_output_templates = all_states.collect{it.run_params}
        assert run_params_output_templates.unique().size() == 1: "The value for the 'run_params' parameter is not the same across runs."
-        def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states]
+
+        def run_metadata_output_templates = all_states.collect{it.run_metadata}
+        assert run_metadata_output_templates.unique().size() == 1: "The value for the 'run_metadata' parameter is not the same across runs."
+
+        def new_state = [
+          "run_params": run_params_output_templates[0],
+          "run_metadata": run_metadata_output_templates[0],
+          "all_states": all_states
+        ]
        return [new_id, new_state]
      }
      | save_params.run(
        key: "save_params_runner",
        fromState: {id, state ->
+
          def convertPaths
          convertPaths = { value ->
            if (value instanceof java.nio.file.Path)
@@ -88,21 +100,32 @@ workflow save_params_wf {
          def yamlString = yaml.dump(convertedState)
          def encodedYaml = yamlString.bytes.encodeBase64().toString()
          
-          def yaml_builder = new org.yaml.snakeyaml.Yaml()
-          def analysis_yaml = yaml_builder.dump(get_workflow_analysis())
-          def encoded_analysis = analysis_yaml.bytes.encodeBase64().toString()
-          
          return [
            "id": id,
            "params_yaml": encodedYaml,
-            "workflow_analysis": encoded_analysis
+            "output": state.run_params
+          ]
+        },
+        toState: ["run_params": "output"]
+      )
+      | save_params.run(
+        key: "save_meta_runner",
+        fromState: {id, state ->
+          def yaml_builder = new org.yaml.snakeyaml.Yaml()
+          def analysis_yaml = yaml_builder.dump(get_workflow_analysis())
+          def encoded_analysis = analysis_yaml.bytes.encodeBase64().toString()
+          return [
+            "id": id,
+            "params_yaml": encoded_analysis,
+            "output": state.run_metadata,
          ]
        },
        toState: { id, output, state ->
-          state + [ run_params: output.output ]
+          state + [ run_metadata: output.output ]
        }
      )

+
  emit:
  output_ch
 }
@@ -301,7 +324,8 @@ workflow run_wf {
          "eset_dir",
          "f_data_dir",
          "p_data_dir",
-          "run_params"
+          "run_params",
+          "run_metadata"
        ]
        def new_state = demux_state + input_state.subMap(keys_to_transfer)

@@ -312,7 +336,8 @@ workflow run_wf {
          "eset_dir",
          "f_data_dir",
          "p_data_dir",
-          "run_params"
+          "run_params",
+          "run_metadata"
        ]
        new_state = new_state.collectEntries{k, v ->
          def newKey = keys_to_rename.contains(k) ? "${k}_workflow" : k
@@ -398,7 +423,10 @@ workflow run_wf {
      // Add the run parameter YAML to the output
      | map {id, grouped_ch_state, _, save_params_state ->
        assert save_params_state.run_params.isFile()
-        def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
+        def new_state = grouped_ch_state + [
+          "run_params": save_params_state.run_params,
+          "run_metadata": save_params_state.run_metadata
+        ]
        return [id, new_state]
      }
      // Group the events in order to publish the results per experiment
@@ -436,8 +464,10 @@ workflow run_wf {
            "f_data_dir_workflow",
            "p_data_dir_workflow",
            "run_params_workflow",
+            "run_metadata_workflow",
            "f_data",
-            "run_params"
+            "run_params",
+            "run_metadata"
          ]
          def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name ->
            argument_values = states.collect{it.get(argument_name)}.unique()
@@ -480,9 +510,11 @@ workflow run_wf {
            p_data: state.p_data,
            html_report: state.html_report,
            run_params: state.run_params,
+            run_metadata: state.run_metadata,
            // Output locations
            html_report_output: "${state.results_prefix}/${state.html_report.name}", 
            run_params_output: "${state.results_prefix}/${state.run_params_workflow}",
+            run_metadata_output: "${state.results_prefix}/${state.run_metadata_workflow}",
            star_output_dir: "${state.results_prefix}/${state.star_output_dir_workflow}",
            nrReadsNrGenesPerChrom_dir: "${state.results_prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}",
            star_qc_metrics_dir: "${state.results_prefix}/${state.star_qc_metrics_dir_workflow}",
@@ -494,6 +526,7 @@ workflow run_wf {
        toState: { id, result, state -> 
          result + [
            "run_params": state.run_params,
+            "run_metadata": state.run_metadata,
            "_meta": ["join_id": state.event_id[0]],
            "results_prefix": state.results_prefix
          ] 
@@ -598,6 +631,7 @@ workflow run_wf {
        "f_data_dir",
        "p_data_dir",
        "run_params",
+        "run_metadata",
        "_meta"
      ]
    )
--- a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "listInputDir"
 namespace: "utils"
-version: "v0.14.6"
+version: "v0.14.7"
 argument_groups:
 - name: "Arguments"
  arguments:
@@ -169,11 +169,11 @@ build_info:
  output: "target/_private/nextflow/utils/listInputDir"
  executable: "target/_private/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -205,7 +205,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/_private/nextflow/utils/listInputDir/_viash.yaml
+++ b/target/_private/nextflow/utils/listInputDir/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/_private/nextflow/utils/listInputDir/main.nf
+++ b/target/_private/nextflow/utils/listInputDir/main.nf
@@ -1,4 +1,4 @@
-// listInputDir v0.14.6
+// listInputDir v0.14.7
 // 
 // 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" : "listInputDir",
  "namespace" : "utils",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "argument_groups" : [
    {
      "name" : "Arguments",
@@ -3236,12 +3236,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/_private/nextflow/utils/listInputDir",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3259,7 +3259,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/_private/nextflow/utils/listInputDir/nextflow.config
+++ b/target/_private/nextflow/utils/listInputDir/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'utils/listInputDir'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'List the contents of a directory and parse contained fastq files'
 }

--- a/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml
+++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "well_fastqs_to_esets"
 namespace: "workflows"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -323,7 +323,7 @@ build_info:
  output: "target/_private/nextflow/workflows/well_fastqs_to_esets"
  executable: "target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
@@ -340,7 +340,7 @@ build_info:
  - "target/nextflow/utils/save_params"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -372,7 +372,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml
+++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf
+++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf
@@ -1,4 +1,4 @@
-// well_fastqs_to_esets v0.14.6
+// well_fastqs_to_esets v0.14.7
 // 
 // 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 = [
  "config": processConfig(readJsonBlob('''{
  "name" : "well_fastqs_to_esets",
  "namespace" : "workflows",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3455,12 +3455,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/_private/nextflow/workflows/well_fastqs_to_esets",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3478,7 +3478,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config
+++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'workflows/well_fastqs_to_esets'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Map a list of FASTQ files (one for each well) to a reference genome and generate count matrices.\nSometimes counts from different FASTQ files need to be concatenated. This is done bases on the sample_id:\nif the sample ID of the two plates are identical, the FASTQ files will we joined _before_ mapping.\n'
  author = 'Dries Schaumont'
 }
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -178,7 +178,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -206,11 +206,11 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -242,7 +242,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/eset/create_eset/_viash.yaml
+++ b/target/executable/eset/create_eset/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_eset v0.14.6
+# create_eset v0.14.7
 # 
 # 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
@@ -456,10 +456,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.14.6"
+  echo "create_eset v0.14.7"
  echo ""
  echo "Arguments:"
  echo "    --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_eset v0.14.6"
+            echo "create_eset v0.14.7"
            exit
            ;;
        --pDataFile)
@@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -154,7 +154,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -183,11 +183,11 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -219,7 +219,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/eset/create_fdata/_viash.yaml
+++ b/target/executable/eset/create_fdata/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_fdata v0.14.6
+# create_fdata v0.14.7
 # 
 # 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
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.14.6"
+  echo "create_fdata v0.14.7"
  echo ""
  echo "Create a fdata file"
  echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_fdata v0.14.6"
+            echo "create_fdata v0.14.7"
            exit
            ;;
        --gtf)
@@ -756,7 +756,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -168,7 +168,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -197,11 +197,11 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -233,7 +233,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/eset/create_pdata/_viash.yaml
+++ b/target/executable/eset/create_pdata/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_pdata v0.14.6
+# create_pdata v0.14.7
 # 
 # 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
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.14.6"
+  echo "create_pdata v0.14.7"
  echo ""
  echo "Create a pdata file by combining the mapping statistics"
  echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_pdata v0.14.6"
+            echo "create_pdata v0.14.7"
            exit
            ;;
        --star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -134,7 +134,7 @@ engines:
  id: "docker"
  image: "bioconductor/bioconductor_docker:3.19"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -155,11 +155,11 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -191,7 +191,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# check_eset v0.14.6
+# check_eset v0.14.7
 # 
 # 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
@@ -455,10 +455,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.14.6"
+  echo "check_eset v0.14.7"
  echo ""
  echo "This component test the ExpressionSet object as output by the main pipeline."
  echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_eset v0.14.6"
+            echo "check_eset v0.14.7"
            exit
            ;;
        --eset)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -141,7 +141,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -164,11 +164,11 @@ build_info:
  output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -200,7 +200,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# check_cutadapt_output v0.14.6
+# check_cutadapt_output v0.14.7
 # 
 # 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
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_cutadapt_output v0.14.6"
+  echo "check_cutadapt_output v0.14.7"
  echo ""
  echo "This component test the cutadapt output from the well_demultiplex subworkflow."
  echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_cutadapt_output v0.14.6"
+            echo "check_cutadapt_output v0.14.7"
            exit
            ;;
        --fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.14.6"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -121,7 +121,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -139,11 +139,11 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -175,7 +175,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/io/publish_fastqs/_viash.yaml
+++ b/target/executable/io/publish_fastqs/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish_fastqs v0.14.6
+# publish_fastqs v0.14.7
 # 
 # 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_fastqs"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:12Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.14.6"
+  echo "publish_fastqs v0.14.7"
  echo ""
  echo "Publish the fastq files per well"
  echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_fastqs v0.14.6"
+            echo "publish_fastqs v0.14.7"
            exit
            ;;
        --input)
@@ -750,7 +750,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.14.6"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -77,6 +77,15 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output directory"
  description: "Determines the name of output directories\n"
  arguments:
@@ -158,6 +167,15 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata_output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
  - type: "file"
    name: "--html_report_output"
    info: null
@@ -261,7 +279,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -279,11 +297,11 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -315,7 +333,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/io/publish_results/_viash.yaml
+++ b/target/executable/io/publish_results/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish_results v0.14.6
+# publish_results v0.14.7
 # 
 # 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_results"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:12Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.14.6"
+  echo "publish_results v0.14.7"
  echo ""
  echo "Publish the results"
  echo ""
@@ -600,6 +600,9 @@ function ViashHelp {
  echo "    --run_params"
  echo "        type: file, required parameter, file must exist"
  echo ""
+  echo "    --run_metadata"
+  echo "        type: file, required parameter, file must exist"
+  echo ""
  echo "Output directory:"
  echo "    Determines the name of output directories"
  echo ""
@@ -633,6 +636,9 @@ function ViashHelp {
  echo "    --run_params_output"
  echo "        type: file, output, file must exist"
  echo ""
+  echo "    --run_metadata_output"
+  echo "        type: file, output, file must exist"
+  echo ""
  echo "    --html_report_output"
  echo "        type: file, output, file must exist"
  echo ""
@@ -683,7 +689,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_results v0.14.6"
+            echo "publish_results v0.14.7"
            exit
            ;;
        --star_output)
@@ -810,6 +816,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_RUN_PARAMS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --run_metadata)
+            [ -n "$VIASH_PAR_RUN_METADATA" ] && ViashError Bad arguments for option \'--run_metadata\': \'$VIASH_PAR_RUN_METADATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_metadata. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --run_metadata=*)
+            [ -n "$VIASH_PAR_RUN_METADATA" ] && ViashError Bad arguments for option \'--run_metadata=*\': \'$VIASH_PAR_RUN_METADATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --star_output_dir)
            [ -n "$VIASH_PAR_STAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--star_output_dir\': \'$VIASH_PAR_STAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STAR_OUTPUT_DIR="$2"
@@ -887,6 +904,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --run_metadata_output)
+            [ -n "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && ViashError Bad arguments for option \'--run_metadata_output\': \'$VIASH_PAR_RUN_METADATA_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA_OUTPUT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_metadata_output. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --run_metadata_output=*)
+            [ -n "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && ViashError Bad arguments for option \'--run_metadata_output=*\': \'$VIASH_PAR_RUN_METADATA_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --html_report_output)
            [ -n "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && ViashError Bad arguments for option \'--html_report_output\': \'$VIASH_PAR_HTML_REPORT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HTML_REPORT_OUTPUT="$2"
@@ -986,7 +1014,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.7'
  fi

  # print dockerfile
@@ -1102,6 +1130,10 @@ if [ -z ${VIASH_PAR_RUN_PARAMS+x} ]; then
  ViashError '--run_params' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
 fi
+if [ -z ${VIASH_PAR_RUN_METADATA+x} ]; then
+  ViashError '--run_metadata' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
 if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
@@ -1228,6 +1260,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS" ]; then
  ViashError "Input file '$VIASH_PAR_RUN_PARAMS' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA" ] && [ ! -e "$VIASH_PAR_RUN_METADATA" ]; then
+  ViashError "Input file '$VIASH_PAR_RUN_METADATA' does not exist."
+  exit 1
+fi

 # check whether parameters values are of the right type
 if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -1325,6 +1361,9 @@ fi
 if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")"
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_METADATA_OUTPUT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_RUN_METADATA_OUTPUT")"
+fi
 if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")"
 fi
@@ -1415,6 +1454,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_PARAMS")" )
  VIASH_PAR_RUN_PARAMS=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS")
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_METADATA")" )
+  VIASH_PAR_RUN_METADATA=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_METADATA")
+fi
 if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_OUTPUT_DIR")" )
  VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_OUTPUT_DIR")
@@ -1450,6 +1493,11 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
  VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_PARAMS_OUTPUT" )
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_METADATA_OUTPUT")" )
+  VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_METADATA_OUTPUT")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_METADATA_OUTPUT" )
+fi
 if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_HTML_REPORT_OUTPUT")" )
  VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_HTML_REPORT_OUTPUT")
@@ -1532,6 +1580,7 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#'
 $( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA+x} ]; then echo "${VIASH_PAR_RUN_METADATA}" | sed "s#'#'\"'\"'#g;s#.*#par_run_metadata='&'#" ; else echo "# par_run_metadata="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi )
@@ -1539,6 +1588,7 @@ $( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed
 $( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_METADATA_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_metadata_output='&'#" ; else echo "# par_run_metadata_output="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
@@ -1581,6 +1631,7 @@ declare -A path_pars_dirs=(
 declare -A path_pars_files=(
  ["par_html_report_output"]="par_html_report"
  ["par_run_params_output"]="par_run_params"
+  ["par_run_metadata_output"]="par_run_metadata"
 )

 echo "Canonicalizing output paths."
@@ -1720,6 +1771,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then
    VIASH_PAR_RUN_PARAMS=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS")
  fi
+  if [ ! -z "$VIASH_PAR_RUN_METADATA" ]; then
+    VIASH_PAR_RUN_METADATA=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_METADATA")
+  fi
  if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
    VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_OUTPUT_DIR")
  fi
@@ -1741,6 +1795,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
    VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
  fi
+  if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then
+    VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_METADATA_OUTPUT")
+  fi
  if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
    VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_HTML_REPORT_OUTPUT")
  fi
@@ -1788,6 +1845,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS_OUTP
  ViashError "Output file '$VIASH_PAR_RUN_PARAMS_OUTPUT' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then
+  ViashError "Output file '$VIASH_PAR_RUN_METADATA_OUTPUT' does not exist."
+  exit 1
+fi
 if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -e "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
  ViashError "Output file '$VIASH_PAR_HTML_REPORT_OUTPUT' does not exist."
  exit 1
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -285,11 +285,11 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -321,7 +321,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/parallel_map/_viash.yaml
+++ b/target/executable/parallel_map/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# parallel_map v0.14.6
+# parallel_map v0.14.7
 # 
 # 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
@@ -461,10 +461,10 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.14.6"
+  echo "parallel_map v0.14.7"
  echo ""
  echo "Map wells in batch, using STAR"
  echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "parallel_map v0.14.6"
+            echo "parallel_map v0.14.7"
            exit
            ;;
        --input_r1)
@@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -168,7 +168,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -225,11 +225,11 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -261,7 +261,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/report/create_report/_viash.yaml
+++ b/target/executable/report/create_report/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_report v0.14.6
+# create_report v0.14.7
 # 
 # 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
@@ -465,10 +465,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:02:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.14.6"
+  echo "create_report v0.14.7"
  echo ""
  echo "Create a basic QC report in HTML format based on a number of esets."
  echo ""
@@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_report v0.14.6"
+            echo "create_report v0.14.7"
            exit
            ;;
        --eset)
@@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -175,7 +175,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -204,11 +204,11 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -240,7 +240,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/stats/combine_star_logs/_viash.yaml
+++ b/target/executable/stats/combine_star_logs/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# combine_star_logs v0.14.6
+# combine_star_logs v0.14.7
 # 
 # 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
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "combine_star_logs v0.14.6"
+  echo "combine_star_logs v0.14.7"
  echo ""
  echo "Arguments:"
  echo "    --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "combine_star_logs v0.14.6"
+            echo "combine_star_logs v0.14.7"
            exit
            ;;
        --barcodes)
@@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -159,7 +159,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -188,11 +188,11 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -224,7 +224,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/stats/generate_pool_statistics/_viash.yaml
+++ b/target/executable/stats/generate_pool_statistics/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# generate_pool_statistics v0.14.6
+# generate_pool_statistics v0.14.7
 # 
 # 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
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_pool_statistics v0.14.6"
+  echo "generate_pool_statistics v0.14.7"
  echo ""
  echo "Arguments:"
  echo "    --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_pool_statistics v0.14.6"
+            echo "generate_pool_statistics v0.14.7"
            exit
            ;;
        --nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -230,7 +230,7 @@ engines:
  id: "docker"
  image: "python:3.13-trixie"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -260,11 +260,11 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -296,7 +296,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/stats/generate_well_statistics/_viash.yaml
+++ b/target/executable/stats/generate_well_statistics/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# generate_well_statistics v0.14.6
+# generate_well_statistics v0.14.7
 # 
 # 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
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:02:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_well_statistics v0.14.6"
+  echo "generate_well_statistics v0.14.7"
  echo ""
  echo "Generate summary statistics from BAM files generated by STAR solo."
  echo ""
@@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_well_statistics v0.14.6"
+            echo "generate_well_statistics v0.14.7"
            exit
            ;;
        --input)
@@ -861,7 +861,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.7'
  fi

  # print dockerfile
--- a/target/executable/utils/save_params/.config.vsh.yaml
+++ b/target/executable/utils/save_params/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "save_params"
 namespace: "utils"
-version: "v0.14.6"
+version: "v0.14.7"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -20,23 +20,14 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
-  - type: "string"
-    name: "--workflow_analysis"
-    description: "Base64 encoded YAML containing workflow analysis information (name\
-      \ and version for all workflows)\n"
-    info: null
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
 - name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "The output YAML file\n"
    info: null
-    default:
-    - "params.yaml"
+    example:
+    - "output.yaml"
    must_exist: true
    create_parent: true
    required: true
@@ -137,7 +128,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -160,11 +151,11 @@ build_info:
  output: "target/executable/utils/save_params"
  executable: "target/executable/utils/save_params/save_params"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -196,7 +187,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/utils/save_params/_viash.yaml
+++ b/target/executable/utils/save_params/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# save_params v0.14.6
+# save_params v0.14.7
 # 
 # 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
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "pyyaml"

 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37"
-LABEL org.opencontainers.image.version="v0.14.6"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"

 VIASHDOCKER
  fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "save_params v0.14.6"
+  echo "save_params v0.14.7"
  echo ""
  echo "Save parameters to a YAML file"
  echo ""
@@ -586,15 +586,10 @@ function ViashHelp {
  echo "        type: string, required parameter"
  echo "        base64 encoded yaml containing the state"
  echo ""
-  echo "    --workflow_analysis"
-  echo "        type: string"
-  echo "        Base64 encoded YAML containing workflow analysis information (name and"
-  echo "        version for all workflows)"
-  echo ""
  echo "Outputs:"
  echo "    --output"
  echo "        type: file, required parameter, output, file must exist"
-  echo "        default: params.yaml"
+  echo "        example: output.yaml"
  echo "        The output YAML file"
  echo ""
  echo "Viash built in Computational Requirements:"
@@ -644,7 +639,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "save_params v0.14.6"
+            echo "save_params v0.14.7"
            exit
            ;;
        --id)
@@ -669,17 +664,6 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_PARAMS_YAML=$(ViashRemoveFlags "$1")
            shift 1
            ;;
-        --workflow_analysis)
-            [ -n "$VIASH_PAR_WORKFLOW_ANALYSIS" ] && ViashError Bad arguments for option \'--workflow_analysis\': \'$VIASH_PAR_WORKFLOW_ANALYSIS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_WORKFLOW_ANALYSIS="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --workflow_analysis. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --workflow_analysis=*)
-            [ -n "$VIASH_PAR_WORKFLOW_ANALYSIS" ] && ViashError Bad arguments for option \'--workflow_analysis=*\': \'$VIASH_PAR_WORKFLOW_ANALYSIS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_WORKFLOW_ANALYSIS=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
@@ -779,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.6'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.7'
  fi

  # print dockerfile
@@ -1072,7 +1056,6 @@ import base64
 par = {
  'id': $( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "r'${VIASH_PAR_ID//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'params_yaml': $( if [ ! -z ${VIASH_PAR_PARAMS_YAML+x} ]; then echo "r'${VIASH_PAR_PARAMS_YAML//\'/\'\"\'\"r\'}'"; else echo None; fi ),
-  'workflow_analysis': $( if [ ! -z ${VIASH_PAR_WORKFLOW_ANALYSIS+x} ]; then echo "r'${VIASH_PAR_WORKFLOW_ANALYSIS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi )
 }
 meta = {
@@ -1101,18 +1084,10 @@ dep = {

 ## VIASH END

-# Custom representer to preserve dict order in YAML output
-# Note: Python 3.7+ dicts maintain insertion order by default
-def represent_dict(dumper, data):
-    return dumper.represent_dict(data.items())
-
 class Dumper(yaml.Dumper):
    def increase_indent(self, flow=False, indentless=False):
        return super(Dumper, self).increase_indent(flow, False)

-# Register the representer for dicts to preserve order
-Dumper.add_representer(dict, represent_dict)
-
 def decode_params_yaml(encoded_yaml):
    yaml_bytes = base64.b64decode(encoded_yaml)
    yaml_string = yaml_bytes.decode('utf-8')
@@ -1122,26 +1097,8 @@ def decode_params_yaml(encoded_yaml):

 params = decode_params_yaml(par['params_yaml'])

-# Build the output structure
-output_data = params  # params is a list of states
-
-# Add workflow analysis information if provided
-if par.get('workflow_analysis'):
-    try:
-        analysis_bytes = base64.b64decode(par['workflow_analysis'])
-        analysis_string = analysis_bytes.decode('utf-8')
-        analysis = yaml.safe_load(analysis_string)
-        # Since params is a list, create a dict wrapper
-        output_data = {
-            'params': params,
-            'analysis': analysis
-        }
-    except (TypeError, ValueError) as e:
-        e.add_note("Could not parse workflow_analysis YAML.")
-        raise
-
 with open(par["output"], 'w') as f:
-    yaml.dump(output_data, f, default_flow_style=False, Dumper=Dumper)
+    yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
 VIASHMAIN
 python -B "\$tempscript" &
 wait "\$!"
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -178,7 +178,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -206,11 +206,11 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -242,7 +242,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/eset/create_eset/_viash.yaml
+++ b/target/nextflow/eset/create_eset/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -1,4 +1,4 @@
-// create_eset v0.14.6
+// create_eset v0.14.7
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_eset",
  "namespace" : "eset",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3271,7 +3271,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3309,12 +3309,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3332,7 +3332,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4217,7 +4217,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/eset/create_eset/nextflow.config
+++ b/target/nextflow/eset/create_eset/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'eset/create_eset'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -154,7 +154,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -183,11 +183,11 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -219,7 +219,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/eset/create_fdata/_viash.yaml
+++ b/target/nextflow/eset/create_fdata/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -1,4 +1,4 @@
-// create_fdata v0.14.6
+// create_fdata v0.14.7
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_fdata",
  "namespace" : "eset",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3279,12 +3279,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3302,7 +3302,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/eset/create_fdata/nextflow.config
+++ b/target/nextflow/eset/create_fdata/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'eset/create_fdata'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Create a fdata file\n'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -168,7 +168,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -197,11 +197,11 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -233,7 +233,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/eset/create_pdata/_viash.yaml
+++ b/target/nextflow/eset/create_pdata/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -1,4 +1,4 @@
-// create_pdata v0.14.6
+// create_pdata v0.14.7
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_pdata",
  "namespace" : "eset",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3252,7 +3252,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3293,12 +3293,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3316,7 +3316,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3812,7 +3812,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/eset/create_pdata/nextflow.config
+++ b/target/nextflow/eset/create_pdata/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'eset/create_pdata'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Create a pdata file by combining the mapping statistics \n'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -134,7 +134,7 @@ engines:
  id: "docker"
  image: "bioconductor/bioconductor_docker:3.19"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -155,11 +155,11 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -191,7 +191,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -1,4 +1,4 @@
-// check_eset v0.14.6
+// check_eset v0.14.7
 // 
 // 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 = [
  "config": processConfig(readJsonBlob('''{
  "name" : "check_eset",
  "namespace" : "integration_test_components/htrnaseq",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3206,7 +3206,7 @@ meta = [
      "id" : "docker",
      "image" : "bioconductor/bioconductor_docker:3.19",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3233,12 +3233,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3256,7 +3256,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3906,7 +3906,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'integration_test_components/htrnaseq/check_eset'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'This component test the ExpressionSet object as output by the main pipeline.'
  author = 'Dries Schaumont'
 }
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -141,7 +141,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -164,11 +164,11 @@ build_info:
  output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -200,7 +200,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -1,4 +1,4 @@
-// check_cutadapt_output v0.14.6
+// check_cutadapt_output v0.14.7
 // 
 // 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 = [
  "config": processConfig(readJsonBlob('''{
  "name" : "check_cutadapt_output",
  "namespace" : "integration_test_components/well_demultiplexing",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3213,7 +3213,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3244,12 +3244,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3267,7 +3267,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3786,7 +3786,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
  author = 'Dries Schaumont'
 }
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.14.6"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -121,7 +121,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -139,11 +139,11 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -175,7 +175,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/io/publish_fastqs/_viash.yaml
+++ b/target/nextflow/io/publish_fastqs/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -1,4 +1,4 @@
-// publish_fastqs v0.14.6
+// publish_fastqs v0.14.7
 // 
 // 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_fastqs",
  "namespace" : "io",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3184,7 +3184,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3207,12 +3207,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3230,7 +3230,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3682,7 +3682,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish_fastqs/nextflow.config
+++ b/target/nextflow/io/publish_fastqs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish_fastqs'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Publish the fastq files per well'
 }

--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.14.6"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -77,6 +77,15 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output directory"
  description: "Determines the name of output directories\n"
  arguments:
@@ -158,6 +167,15 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata_output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
  - type: "file"
    name: "--html_report_output"
    info: null
@@ -261,7 +279,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -279,11 +297,11 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -315,7 +333,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/io/publish_results/_viash.yaml
+++ b/target/nextflow/io/publish_results/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -1,4 +1,4 @@
-// publish_results v0.14.6
+// publish_results v0.14.7
 // 
 // 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_results",
  "namespace" : "io",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3117,6 +3117,16 @@ meta = [
          "direction" : "input",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--run_metadata",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -3218,6 +3228,16 @@ meta = [
          "multiple" : false,
          "multiple_sep" : ";"
        },
+        {
+          "type" : "file",
+          "name" : "--run_metadata_output",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
        {
          "type" : "file",
          "name" : "--html_report_output",
@@ -3346,7 +3366,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3369,12 +3389,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3392,7 +3412,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3433,6 +3453,7 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#'
 $( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA+x} ]; then echo "${VIASH_PAR_RUN_METADATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_metadata='&'#" ; else echo "# par_run_metadata="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi )
@@ -3440,6 +3461,7 @@ $( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed
 $( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_METADATA_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_metadata_output='&'#" ; else echo "# par_run_metadata_output="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
@@ -3482,6 +3504,7 @@ declare -A path_pars_dirs=(
 declare -A path_pars_files=(
  ["par_html_report_output"]="par_html_report"
  ["par_run_params_output"]="par_run_params"
+  ["par_run_metadata_output"]="par_run_metadata"
 )

 echo "Canonicalizing output paths."
@@ -3909,7 +3932,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish_results/nextflow.config
+++ b/target/nextflow/io/publish_results/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish_results'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Publish the results'
 }

--- a/target/nextflow/io/publish_results/nextflow_schema.json
+++ b/target/nextflow/io/publish_results/nextflow_schema.json
@@ -82,6 +82,13 @@
          "exists": true,
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
+        },
+        "run_metadata": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
@@ -146,6 +153,13 @@
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_params_output\"`, direction: `output`. ",
          "default": "$id.$key.run_params_output"
        },
+        "run_metadata_output": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_metadata_output\"`, direction: `output`. ",
+          "default": "$id.$key.run_metadata_output"
+        },
        "html_report_output": {
          "type": "string",
          "format": "path",
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -285,11 +285,11 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -321,7 +321,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/parallel_map/_viash.yaml
+++ b/target/nextflow/parallel_map/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -1,4 +1,4 @@
-// parallel_map v0.14.6
+// parallel_map v0.14.7
 // 
 // 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" : "parallel_map",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3332,7 +3332,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3379,12 +3379,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3402,7 +3402,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4173,7 +4173,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/parallel_map/nextflow.config
+++ b/target/nextflow/parallel_map/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'parallel_map'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n'
  author = 'Dries Schaumont, Toni Verbeiren'
 }
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -168,7 +168,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -225,11 +225,11 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -261,7 +261,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/report/create_report/_viash.yaml
+++ b/target/nextflow/report/create_report/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -1,4 +1,4 @@
-// create_report v0.14.6
+// create_report v0.14.7
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_report",
  "namespace" : "report",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3261,7 +3261,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3334,12 +3334,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3357,7 +3357,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3849,7 +3849,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/report/create_report",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/report/create_report/nextflow.config
+++ b/target/nextflow/report/create_report/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'report/create_report'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  description = 'Create a basic QC report in HTML format based on a number of esets.\n'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -175,7 +175,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -204,11 +204,11 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -240,7 +240,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/stats/combine_star_logs/_viash.yaml
+++ b/target/nextflow/stats/combine_star_logs/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -1,4 +1,4 @@
-// combine_star_logs v0.14.6
+// combine_star_logs v0.14.7
 // 
 // 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 = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_star_logs",
  "namespace" : "stats",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3254,7 +3254,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3295,12 +3295,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3318,7 +3318,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3977,7 +3977,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/combine_star_logs",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/stats/combine_star_logs/nextflow.config
+++ b/target/nextflow/stats/combine_star_logs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'stats/combine_star_logs'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  author = 'Dries Schaumont'
 }

--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.14.6"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -159,7 +159,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.6"
+  target_tag: "v0.14.7"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -188,11 +188,11 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.4"
-  git_commit: "9346c55e3f894994935b0928759dca9e56866d37"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.6"
+  version: "v0.14.7"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -224,7 +224,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.6'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/stats/generate_pool_statistics/_viash.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.6
+version: v0.14.7
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -1,4 +1,4 @@
-// generate_pool_statistics v0.14.6
+// generate_pool_statistics v0.14.7
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "generate_pool_statistics",
  "namespace" : "stats",
-  "version" : "v0.14.6",
+  "version" : "v0.14.7",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.6",
+      "target_tag" : "v0.14.7",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3279,12 +3279,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.4",
-    "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.6",
+    "version" : "v0.14.7",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3302,7 +3302,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'v0.14.6'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3832,7 +3832,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/generate_pool_statistics",
-    "tag" : "v0.14.6"
+    "tag" : "v0.14.7"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/stats/generate_pool_statistics/nextflow.config
+++ b/target/nextflow/stats/generate_pool_statistics/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'stats/generate_pool_statistics'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.6'
+  version = 'v0.14.7'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

--- a/Show More
+++ b/Show More