Build branch htrnaseq/v0.14 with version v0.14.2 to htrnaseq on branch v0.14 (40230f8)

Build pipeline: viash-hub.htrnaseq.v0.14.2-ws9m8 Source commit: 40230f83ee Source message: Bump version to v0.14.2
2025-11-27 09:39:23 +00:00
parent c909aaf9a8
commit 3817ff8d16
124 changed files with 693 additions and 524 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,11 @@
+# htrnaseq v0.14.2
+
+# Bug fixes
+
+* Fix esets not being created when processing multiple samples from a single run (PR #92).
+
+* Publishing a very small amount of data no longer throws an error (calling `dropRight` on a `null` object) (PR #92). 
+
 # htrnaseq v0.14.1

 # Minor changes
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/src/workflows/runner/integration_test.sh
+++ b/src/workflows/runner/integration_test.sh
@@ -37,4 +37,12 @@ nextflow \
  -config ./src/config/labels.config \
  -entry test_same_experiment_id_different_projects_wf \
  -resume \
+  -profile docker,local
+
+nextflow \
+  run . \
+  -main-script src/workflows/runner/test.nf \
+  -config ./src/config/labels.config \
+  -entry test_multiple_samples \
+  -resume \
  -profile docker,local
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -243,7 +243,7 @@ workflow run_wf {
    This will cause the the `well_fastqs_to_esets` workflow to do the grouping and concatenation of the 
    events with the same sample ID.
    */
-    htrnaseq_ch = demultiplex_ch
+    demultiplex_with_input_ids_ch = demultiplex_ch
      // The IDs in the demultiplex_ch are of format '<run_id>/<sample_id>' (not split per experiment.)
      | flatMap {id, state ->
        state.event_ids.collect{ event_id ->
@@ -252,8 +252,12 @@ workflow run_wf {
        }
      }
      // The event IDs at this point are the same IDs in the `input_ch` in order to do the join
-      | join(input_ch)
-      | map {event_id, demux_state, input_state ->
+
+    htrnaseq_ch = input_ch
+      | cross(demultiplex_with_input_ids_ch)
+      | map {input_event, demux_event  ->
+        def (event_id, demux_state) = demux_event
+        def input_state = input_event[1] 
        def keys_to_transfer = [
          "umi_length",
          "annotation",
@@ -491,7 +495,7 @@ workflow run_wf {
  awaited_events_ch = results_publish_ch.mix(fastq_publish_ch)
    | toSortedList()
    | map {states ->
-      if (states.size == 0) {
+      if (states.size() == 0) {
        has_published.compareAndSet(false, true)
        error("There seems to be nothing to publish!")
      }
@@ -503,6 +507,12 @@ workflow run_wf {
    // Create periodic events in order to check for the publishing to be done
    | combine(interval_at_least_one_event_ch)
    | until { event ->
+      // Prevent until to output nothing by stopping on the first item of the channel.
+      // It will output 'null' when its the first iteration.
+      // This happens when there is not a lot of data to publish and/or the transfer is fast.
+      if (event[-1] == 0) {
+        return false
+      }
      println("Checking if publishing has finished in service ${service}")
      def running_tasks = null
      if(service instanceof ThreadPoolExecutor) {
--- a/src/workflows/runner/test.nf
+++ b/src/workflows/runner/test.nf
@@ -694,3 +694,136 @@ workflow test_same_experiment_id_different_projects_wf {
        }
    }
 }
+
+
+
+workflow test_multiple_samples {
+  
+  /*
+  Test a sequencing run with multiple samples
+  */
+
+  pipeline_version = get_version(viash_config)
+  resources_test = file(params.resources_test)
+
+  // results_publish_dir and results_publish_dir are inherited using params
+  // but they must be defined in the state as well because viash will check
+  // if all arguments are present in the hashmap
+  output_ch = Channel.fromList([
+    [
+        id: "run_1_exp_bar",
+        run_id: "run_1",
+        input: resources_test.resolve("10k_multiple_samples/SRR14730301_SRR14730302"),
+        genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
+        barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
+        annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
+        project_id: "foo",
+        experiment_id: "bar",
+        fastq_publish_dir: params.fastq_publish_dir,
+        results_publish_dir: params.results_publish_dir,
+    ],
+  ])
+  | map { state -> [state.id, state]}
+  | runner.run(
+    toState: { id, output, state -> output + [orig_input: state.input] }
+  )
+  | view { output ->
+    assert output.size() == 2 : "outputs should contain two elements; [id, file]"
+    "Output: $output"
+  }
+
+  tosortedlistch = output_ch
+    | toSortedList()
+    | map {events ->
+        assert events.size() == 1, "Expected 2 events to be output, found ${events.size()}"
+        events
+    }
+    | map {states -> 
+        def output_state = states.find{id, _ -> id == "foo/bar"}[1]
+        assert output_state.eset_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.rds", "VH02001614.rds"].toSet()
+        assert output_state.star_output_dir.listFiles().collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
+        ["VH02001612", "VH02001614"].each{it ->
+           assert output_state.star_output_dir.resolve(it).toRealPath().listFiles().collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+        }
+        assert output_state.star_qc_metrics_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
+        assert output_state.nrReadsNrGenesPerChrom_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
+        assert output_state.run_params.isFile()
+    }
+
+
+    workflow.onComplete = {
+        try {
+            // Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
+            // So in order for the assert statement to work (or allow other errors to let the tests to fail)
+            // We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
+            // The error message will show up in .nextflow.log
+            def fastq_subdir = file("${params.fastq_publish_dir}")
+            assert fastq_subdir.isDirectory()
+            def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
+            def expected_run_folders = ["run_1"].toSet()
+            assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
+            unique_dirs = [
+                "run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
+            ]
+            assert unique_dirs.every{it.value.size() == 1}
+            unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
+
+            assert unique_dirs.every{it.value.isDirectory()}
+            assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
+            def expected_samples = [
+                "run1": ["VH02001612", "VH02001614"]
+            ]
+
+            unique_dirs.each{_key, _value ->
+                def samples = expected_samples[_key]
+                samples.each {expected_sample ->
+                    def expected_sample_dir = _value.resolve(expected_sample)
+                    assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
+                    def expected_fastq_files = [
+                        "A1_R1_001.fastq.gz", "A1_R2_001.fastq.gz", 
+                        "B1_R1_001.fastq.gz", "B1_R2_001.fastq.gz",
+                        "unknown_R1_001.fastq.gz", "unknown_R2_001.fastq.gz"]
+                    def found_files = files("${expected_sample_dir}/*.fastq.gz", type: 'any')
+                    assert found_files.every{it.isFile()}
+                    assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
+                }
+            }
+
+            // Experiment foo/bar
+            def results_subdir = file("${params.results_publish_dir}")
+            assert fastq_subdir.isDirectory()
+            def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
+            assert expected_subdir.isDirectory()
+            def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
+            assert expected_result_dir.size() == 1
+            expected_result_dir = expected_result_dir[0]
+            assert expected_result_dir.isDirectory()
+            def expected_esets = ["VH02001612.rds", "VH02001614.rds"]
+            def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
+            assert found_esets.size() == 2
+            assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
+            expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"]
+            def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
+            assert found_pdata.size() == 2
+            assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
+            def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
+            assert found_nr_genes_nr_reads.size() == 2
+            assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet() 
+            def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
+            assert found_star_logs.size() == 2
+            assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
+            def star_output = file("${expected_result_dir}/star_output", type: 'any')
+            assert star_output.isDirectory()
+            
+            assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
+            assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+            assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+            assert file("${expected_result_dir}/report.html").isFile()
+            assert file("${expected_result_dir}/params.yaml").isFile()
+            assert file("${expected_result_dir}/fData/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
+
+        } catch (Exception e) {
+            throw new WorkflowScriptErrorException("Integration test failed!", e)
+        }
+    }
+}
--- 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: "v0.14.1"
+version: "v0.14.2"
 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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -193,7 +193,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/_private/nextflow/utils/listInputDir/main.nf
+++ b/target/_private/nextflow/utils/listInputDir/main.nf
@@ -1,4 +1,4 @@
-// listInputDir v0.14.1
+// listInputDir v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "argument_groups" : [
    {
      "name" : "Arguments",
@@ -3236,18 +3236,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/_private/nextflow/utils/listInputDir",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -313,7 +313,7 @@ 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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
@@ -330,7 +330,7 @@ build_info:
  - "target/nextflow/utils/save_params"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -350,7 +350,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -362,7 +362,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+// well_fastqs_to_esets v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3444,18 +3444,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/_private/nextflow/workflows/well_fastqs_to_esets",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -3467,7 +3467,7 @@ 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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -230,7 +230,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# create_eset v0.14.2
 # 
 # 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="2025-11-20T19:48:24Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.14.1"
+  echo "create_eset v0.14.2"
  echo ""
  echo "Arguments:"
  echo "    --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_eset v0.14.1"
+            echo "create_eset v0.14.2"
            exit
            ;;
        --pDataFile)
@@ -794,7 +794,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -207,7 +207,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# create_fdata v0.14.2
 # 
 # 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="2025-11-20T19:48:24Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.14.1"
+  echo "create_fdata v0.14.2"
  echo ""
  echo "Create a fdata file"
  echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_fdata v0.14.1"
+            echo "create_fdata v0.14.2"
            exit
            ;;
        --gtf)
@@ -756,7 +756,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -221,7 +221,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# create_pdata v0.14.2
 # 
 # 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="2025-11-20T19:48:24Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.14.1"
+  echo "create_pdata v0.14.2"
  echo ""
  echo "Create a pdata file by combining the mapping statistics"
  echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_pdata v0.14.1"
+            echo "create_pdata v0.14.2"
            exit
            ;;
        --star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -179,7 +179,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# check_eset v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.14.1"
+  echo "check_eset v0.14.2"
  echo ""
  echo "This component test the ExpressionSet object as output by the main pipeline."
  echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_eset v0.14.1"
+            echo "check_eset v0.14.2"
            exit
            ;;
        --eset)
@@ -754,7 +754,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -188,7 +188,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# check_cutadapt_output v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

 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 v0.14.1"
+  echo "check_cutadapt_output v0.14.2"
  echo ""
  echo "This component test the cutadapt output from the well_demultiplex subworkflow."
  echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_cutadapt_output v0.14.1"
+            echo "check_cutadapt_output v0.14.2"
            exit
            ;;
        --fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -163,7 +163,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# publish_fastqs v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.14.1"
+  echo "publish_fastqs v0.14.2"
  echo ""
  echo "Publish the fastq files per well"
  echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_fastqs v0.14.1"
+            echo "publish_fastqs v0.14.2"
            exit
            ;;
        --input)
@@ -750,7 +750,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -261,7 +261,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -279,11 +279,11 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -303,7 +303,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -315,7 +315,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# publish_results v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.14.1"
+  echo "publish_results v0.14.2"
  echo ""
  echo "Publish the results"
  echo ""
@@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_results v0.14.1"
+            echo "publish_results v0.14.2"
            exit
            ;;
        --star_output)
@@ -986,7 +986,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.2'
  fi

  # print dockerfile
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.14.1"
+version: "v0.14.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -309,7 +309,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/parallel_map/_viash.yaml
+++ b/target/executable/parallel_map/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# parallel_map v0.14.1
+# parallel_map v0.14.2
 # 
 # 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="2025-11-20T19:48:26Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.14.1"
+  echo "parallel_map v0.14.2"
  echo ""
  echo "Map wells in batch, using STAR"
  echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "parallel_map v0.14.1"
+            echo "parallel_map v0.14.2"
            exit
            ;;
        --input_r1)
@@ -907,7 +907,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -159,7 +159,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -215,11 +215,11 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -239,7 +239,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -251,7 +251,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# create_report v0.14.2
 # 
 # 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="2025-11-20T19:48:23Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.14.1"
+  echo "create_report v0.14.2"
  echo ""
  echo "Create a basic QC report in HTML format based on a number of esets."
  echo ""
@@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_report v0.14.1"
+            echo "create_report v0.14.2"
            exit
            ;;
        --eset)
@@ -763,7 +763,7 @@ if [[ "$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/report/create_report:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -228,7 +228,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# combine_star_logs v0.14.2
 # 
 # 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="2025-11-20T19:48:23Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

 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 v0.14.1"
+  echo "combine_star_logs v0.14.2"
  echo ""
  echo "Arguments:"
  echo "    --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "combine_star_logs v0.14.1"
+            echo "combine_star_logs v0.14.2"
            exit
            ;;
        --barcodes)
@@ -825,7 +825,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -212,7 +212,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# generate_pool_statistics v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

 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 v0.14.1"
+  echo "generate_pool_statistics v0.14.2"
  echo ""
  echo "Arguments:"
  echo "    --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_pool_statistics v0.14.1"
+            echo "generate_pool_statistics v0.14.2"
            exit
            ;;
        --nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -284,7 +284,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# generate_well_statistics v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

 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 v0.14.1"
+  echo "generate_well_statistics v0.14.2"
  echo ""
  echo "Generate summary statistics from BAM files generated by STAR solo."
  echo ""
@@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_well_statistics v0.14.1"
+            echo "generate_well_statistics v0.14.2"
            exit
            ;;
        --input)
@@ -861,7 +861,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -128,7 +128,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -151,11 +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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -187,7 +187,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+# save_params v0.14.2
 # 
 # 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="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb"
+LABEL org.opencontainers.image.version="v0.14.2"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "save_params v0.14.1"
+  echo "save_params v0.14.2"
  echo ""
  echo "Save parameters to a YAML file"
  echo ""
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "save_params v0.14.1"
+            echo "save_params v0.14.2"
            exit
            ;;
        --id)
@@ -763,7 +763,7 @@ if [[ "$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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.2'
  fi

  # print dockerfile
--- 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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -230,7 +230,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -1,4 +1,4 @@
-// create_eset v0.14.1
+// create_eset v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3271,7 +3271,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3309,18 +3309,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4207,7 +4207,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -207,7 +207,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -1,4 +1,4 @@
-// create_fdata v0.14.1
+// create_fdata v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3279,18 +3279,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -221,7 +221,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -1,4 +1,4 @@
-// create_pdata v0.14.1
+// create_pdata v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3252,7 +3252,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3293,18 +3293,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3812,7 +3812,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -179,7 +179,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+// check_eset v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "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" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3233,18 +3233,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3906,7 +3906,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -188,7 +188,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+// check_cutadapt_output v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3213,7 +3213,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3244,18 +3244,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "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" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -163,7 +163,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -1,4 +1,4 @@
-// publish_fastqs v0.14.1
+// publish_fastqs v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3184,7 +3184,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3207,18 +3207,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3682,7 +3682,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -261,7 +261,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -279,11 +279,11 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -303,7 +303,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -315,7 +315,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -1,4 +1,4 @@
-// publish_results v0.14.1
+// publish_results v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3346,7 +3346,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3369,18 +3369,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -3392,7 +3392,7 @@ 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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3909,7 +3909,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  description = 'Publish the results'
 }

--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.14.1"
+version: "v0.14.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -309,7 +309,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/parallel_map/_viash.yaml
+++ b/target/nextflow/parallel_map/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -1,4 +1,4 @@
-// parallel_map v0.14.1
+// parallel_map v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3332,7 +3332,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3379,18 +3379,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4171,7 +4171,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -159,7 +159,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -215,11 +215,11 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -239,7 +239,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -251,7 +251,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -1,4 +1,4 @@
-// create_report v0.14.1
+// create_report v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3251,7 +3251,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3323,18 +3323,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -3346,7 +3346,7 @@ 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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3831,7 +3831,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/report/create_report",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -228,7 +228,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+// combine_star_logs v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3254,7 +3254,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3295,18 +3295,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3977,7 +3977,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/combine_star_logs",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  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: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -212,7 +212,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  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: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- 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 v0.14.1
+// generate_pool_statistics v0.14.2
 // 
 // 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" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3279,18 +3279,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3832,7 +3832,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/generate_pool_statistics",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "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 = 'v0.14.1'
+  version = 'v0.14.2'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.14.1"
+version: "v0.14.2"
 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: "v0.14.1"
+  target_tag: "v0.14.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -260,11 +260,11 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.2"
  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\
@@ -284,7 +284,7 @@ package_config:
    \ first.\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
      dest: "resources_test"
  viash_version: "0.9.4"
  source: "src"
@@ -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 := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/stats/generate_well_statistics/_viash.yaml
+++ b/target/nextflow/stats/generate_well_statistics/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.2
 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"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
  test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
      dest: resources_test
 config_mods: |
  .requirements.commands := ['ps']
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -1,4 +1,4 @@
-// generate_well_statistics v0.14.1
+// generate_well_statistics v0.14.2
 // 
 // 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_well_statistics",
  "namespace" : "stats",
-  "version" : "v0.14.1",
+  "version" : "v0.14.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3319,7 +3319,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.13-trixie",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3361,18 +3361,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.2",
    "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" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
          "dest" : "resources_test"
        }
      ]
@@ -3384,7 +3384,7 @@ 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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.2'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3905,7 +3905,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/generate_well_statistics",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/stats/generate_well_statistics/nextflow.config
+++ b/target/nextflow/stats/generate_well_statistics/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'stats/generate_well_statistics'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.2'
  description = 'Generate summary statistics from BAM files generated by STAR solo.'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/Show More
+++ b/Show More