Build branch htrnaseq/v0.14 with version v0.14.4 to htrnaseq on branch v0.14 (2a509fa)

Build pipeline: viash-hub.htrnaseq.v0.14.4-n6dwv Source commit: 2a509fa7ae Source message: Bump version to v0.14.4
2025-12-12 14:40:11 +00:00
parent 921e84a799
commit c824346bbd
133 changed files with 796 additions and 447 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -14,6 +14,7 @@ work
 # R related files
 .Rproj.user
 htrnaseq.Rproj
+.Rhistory

 # vscode
 .vscode
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# htrnaseq v0.14.4
+
+## New functionality
+
+* `report`: show preprocessing parameters and the number of mapped reads per UMI in a visual (PR #97).
+
 # htrnaseq v0.14.3

 ## Bug fixes
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/src/report/config.vsh.yaml
+++ b/src/report/config.vsh.yaml
@@ -14,6 +14,8 @@ argument_groups:
      name: "--eset"
      required: true
      multiple: true
+    - type: file
+      name: "--preproc_params"
    - type: file
      name: "--output_report"
      required: true
@@ -63,6 +65,7 @@ engines:
          - DT
          - logger
          - bit64
+          - yaml
        script:
          - install.packages("oaStyle", repos = c(rdepot = "https://repos.openanalytics.eu/repo/public", getOption("repos")))
    test_setup:
@@ -72,6 +75,4 @@ engines:
          - R.utils
 runners:
  - type: executable
-  - type: nextflow
-
-     
+  - type: nextflow
--- a/src/report/script.R
+++ b/src/report/script.R
@@ -12,6 +12,11 @@ esets_normalized <- lapply(par$eset, function(eset_path) {
  return(file.path(normalizePath(dirname(eset_path)), basename(eset_path)))
 })

+preproc_params_normalized <- NULL
+if(!is.null(par$preproc_params)){
+  preproc_params_normalized <- file.path(normalizePath(dirname(par$preproc_params)), basename(par$preproc_params))
+}
+
 log_info(paste0(
  "Rendering markdown {template} to HTML ",
  "{par$output_report} with esets {paste(esets_normalized, collapse = ', ')}"
@@ -26,6 +31,7 @@ rmarkdown::render(
  clean = TRUE,
  params = list(
    esets = esets_normalized,
+    preproc_params = preproc_params_normalized,
    outputDir = par$report_dir
  )
 )
--- a/src/report/template.Rmd
+++ b/src/report/template.Rmd
@@ -11,6 +11,8 @@ params:
  esets:
    - sample1.rds
    - sample2.rds
+  preproc_params:
+    - params.yaml  
 ---

 <!---
@@ -32,9 +34,11 @@ div.main-container {



-```{r params, eval = TRUE, include = FALSE}
+```{r get_params, eval = TRUE, include = FALSE}
 outputDir <- params$outputDir
 esets <- params$esets
+preproc_params_file <- params$preproc_params
+
 ```


@@ -91,6 +95,7 @@ library(knitr)
 library(Biobase)
 library(gridExtra)
 library(RColorBrewer)
+library(yaml)
 ```


@@ -115,6 +120,7 @@ names(esetList) <- unlist(pools)
 # Create qcData
 pDataList <- lapply(esetList, function(eset) data.table(pData(eset)))
 qcData <- rbindlist(pDataList, fill = TRUE)
+qcData[, nMappedReads_per_UMI :=  NumberOfMappedReads/NumberOfUMIs]

 textVars <- "SampleName"
 annotationVar <- "PoolName"
@@ -178,6 +184,30 @@ if (length(Design_levels) == 1) {
 }
 ```

+
+
+```{r versions_and_params, results="asis", eval = !is.null(preproc_params_file)}
+
+preproc_params <- gsub(" ", "", unlist(read_yaml(preproc_params_file)))
+
+cat("# Parameters", "\n\n",
+    "<blockquote>", "\n\n",
+    "**The preprocessing parameters were: ** <br>",
+    "`project id: ", preproc_params["project_id"],"`  \n",
+    "`experiment id: ", preproc_params["experiment_id"],"`  \n",
+    "`run id: ", preproc_params["run_id"],"` \n",
+    "`raw data location: ", preproc_params["input"], "`  \n",
+    "`well barcodes: ", preproc_params["barcodesFasta"],"`  \n",
+    "`genome reference: ", preproc_params["genomeDir"],"`  \n",
+    "`gtf annotation: ", preproc_params["annotation"],"`  \n",
+    "`UMI length: ", preproc_params["umi_length"], "`",
+    "</blockquote>",sep="")
+
+
+```
+
+
+
 # Pool Description

 Per pool within this study, there are several pool layout plots shown, based on the
@@ -420,7 +450,7 @@ ggplot(

 #### Density distribution {.unnumbered}

-```{r density_numberOfUMIs}
+```{r density_numberOfUMIs, fig.width=min(c(14, length(unique(qcData$PoolName))*7)), fig.width=min(c(32, length(unique(qcData$PoolName))*7)),}

 ## Pre-filtering data exploration
 dt_plot <- melt(
@@ -432,7 +462,7 @@ dt_plot <- melt(
 readsDensity_plot <- ggplot(dt_plot, aes(value))
 readsDensity_plot <- readsDensity_plot +
  geom_density(aes(fill = variable), alpha=0.8) +
-  facet_grid(~ PoolName, scales = "free_x", space = "fixed", drop = TRUE) +
+  facet_wrap(~ PoolName, scales = "free_x", space = "fixed", drop = TRUE, ncol = 4) +
  geom_vline(
    xintercept = 5e5,
    linetype = "dashed",
@@ -482,6 +512,9 @@ readsDensity_plot

 ```

+
+
+
 ### Number of Genes {.tabset .unnumbered}

 #### Distribution {.unnumbered}
@@ -601,6 +634,26 @@ ggplot(

 ```

+#### Number of Mapped Reads Per UMI {.unnumbered}
+
+```{r mapping_efficiency_5_plate, fig.height = 7}
+ 
+ ggplot(qcData, aes(x = nMappedReads_per_UMI, y = NumberOfMappedReads, colour = PoolName)) + 
+  geom_point() + 
+  xlab('Number of Mapped Reads per UMI') + ylab("Number of Mapped Reads") +
+  ggtitle('Number of Mapped Reads per UMI vs Number of Mapped Reads') + 
+  theme(strip.text.x = element_text(size = 20),
+        panel.spacing = unit(2, "lines"), 
+        text = element_text(size=10), 
+        axis.text = element_text(angle = 90,size = 15), 
+        plot.title = element_text(size=18), 
+        legend.text = element_text(size=15), 
+        legend.title = element_text(size = 17), 
+        axis.title = element_text(size = 15))
+
+
+```
+
 ### Counting Efficiency {.tabset .unnumbered}

 #### Number of Mapped Reads {.unnumbered}
@@ -647,6 +700,23 @@ ggplot(



+#### Number of Mapped Reads per UMI {.unnumbered}
+
+```{r gene_efficiency_3_plate, fig.height = 7} 
+
+ggplot(qcData, aes(x = nMappedReads_per_UMI, y = NumberOfGenes, colour = PoolName)) + geom_point() + 
+     ylab('Number of Genes') + xlab("Number of Mapped Reads per UMI") + ggtitle('Number of Genes vs Number of Mapped Reads per UMI') + 
+  theme(strip.text.x = element_text(size = 20),
+        panel.spacing = unit(2, "lines"), 
+        text = element_text(size=10), 
+        axis.text = element_text(angle = 90,size = 15), 
+        plot.title = element_text(size=18), 
+        legend.text = element_text(size=15), 
+        legend.title = element_text(size = 17), 
+        axis.title = element_text(size = 15))
+
+
+```
 ## Sequencing Saturation {.tabset}

 The barplots below represent the sequencing saturation per sample as determined by STAR, split per pool. 
--- a/src/report/test.R
+++ b/src/report/test.R
@@ -27,14 +27,18 @@ cat(">> Running component create_report with symbolic links \n")

 link_sample_1 <- file.path(temp_folder, "eset.sample_one.rds")
 link_sample_2 <- file.path(temp_folder, "eset.sample_two.rds")
+link_params <- file.path(temp_folder, "params.yaml")
 createLink(link = link_sample_1,
           target = file.path(meta$resources_dir, "test_data", "eset.sample_one.rds"))
 createLink(link = link_sample_2,
           target = file.path(meta$resources_dir, "test_data", "eset.sample_two.rds"))
+createLink(link = link_params,
+           target = file.path(meta$resources_dir, "test_data", "params.yaml"))

 out <- processx::run(meta$executable, c(
  "--eset", link_sample_1,
  "--eset", link_sample_2,
+  "--preproc_params", link_params,
  "--output_report", "report2.html"
 ))

--- a/src/report/test_data/params.yaml
+++ b/src/report/test_data/params.yaml
@@ -0,0 +1,17 @@
+- annotation: Homo_sapiens.gtf
+  barcodesFasta: barcodes.fasta
+  eset_dir: esets
+  experiment_id: expID
+  f_data_dir: fData
+  fastq_publish_dir: fastqDir
+  genomeDir: /Homo_sapiens/
+  input: /My/fastq/Files
+  nrReadsNrGenesPerChrom_dir: nrReadsNrGenesPerChrom
+  p_data_dir: pData
+  project_id: projID
+  results_publish_dir: projects
+  run_id: runID
+  run_params: params.yaml
+  star_output_dir: star_output
+  star_qc_metrics_dir: starLogs
+  umi_length: 7
--- a/src/workflows/htrnaseq/main.nf
+++ b/src/workflows/htrnaseq/main.nf
@@ -140,7 +140,8 @@ workflow run_wf {
          "eset": "eset",
          "f_data": "f_data",
          "p_data": "p_data",
-          "html_report": "html_report"
+          "html_report": "html_report",
+          "run_params": "run_params"
        ],
        toState: {id, result, state -> state + result}
      )
--- a/src/workflows/well_fastqs_to_esets/config.vsh.yaml
+++ b/src/workflows/well_fastqs_to_esets/config.vsh.yaml
@@ -45,6 +45,11 @@ argument_groups:
          Sample ID for the provided input files. If not provided, the value of --id
          will be used. Input files will allways be demultiplexed separately,
          but the FASTQs for wells with matching sample IDs will be concatenated before mapping.
+      - name: --run_params
+        type: file
+        required: false
+        description: |
+          file with the processing parameters
  - name: Output arguments
    arguments:
      - name: --star_output
--- a/src/workflows/well_fastqs_to_esets/main.nf
+++ b/src/workflows/well_fastqs_to_esets/main.nf
@@ -253,6 +253,7 @@ workflow run_wf {
      | create_report.run(
        fromState: [
          "eset": "esets",
+          "preproc_params" : "run_params",
          "output_report": "html_report",
        ],
        toState: [
@@ -281,7 +282,6 @@ workflow run_wf {
        "f_data": "f_data",
        "p_data": "p_data",
        "html_report": "html_report",
-        "run_params": "run_params",
        "_meta": "_meta",
      ])

--- a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "listInputDir"
 namespace: "utils"
-version: "v0.14.3"
+version: "v0.14.4"
 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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -205,7 +205,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/_private/nextflow/utils/listInputDir/main.nf
+++ b/target/_private/nextflow/utils/listInputDir/main.nf
@@ -1,4 +1,4 @@
-// listInputDir v0.14.3
+// listInputDir v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "listInputDir",
  "namespace" : "utils",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "argument_groups" : [
    {
      "name" : "Arguments",
@@ -3236,12 +3236,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/_private/nextflow/utils/listInputDir",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3259,7 +3259,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -87,6 +87,16 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--run_params"
+    description: "file with the processing parameters\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output arguments"
  arguments:
  - type: "file"
@@ -313,7 +323,7 @@ build_info:
  output: "target/_private/nextflow/workflows/well_fastqs_to_esets"
  executable: "target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf"
  viash_version: "0.9.4"
-  git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
@@ -330,7 +340,7 @@ build_info:
  - "target/nextflow/utils/save_params"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  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\
@@ -362,7 +372,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf
+++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf
@@ -1,4 +1,4 @@
-// well_fastqs_to_esets v0.14.3
+// well_fastqs_to_esets v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "well_fastqs_to_esets",
  "namespace" : "workflows",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3136,6 +3136,17 @@ meta = [
          "direction" : "input",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--run_params",
+          "description" : "file with the processing parameters\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -3444,12 +3455,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/_private/nextflow/workflows/well_fastqs_to_esets",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "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" : {
@@ -3467,7 +3478,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3761,6 +3772,7 @@ workflow run_wf {
      | create_report.run(
        fromState: [
          "eset": "esets",
+          "preproc_params" : "run_params",
          "output_report": "html_report",
        ],
        toState: [
@@ -3789,7 +3801,6 @@ workflow run_wf {
        "f_data": "f_data",
        "p_data": "p_data",
        "html_report": "html_report",
-        "run_params": "run_params",
        "_meta": "_meta",
      ])

--- 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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -242,7 +242,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_eset v0.14.3
+# create_eset v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:50Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.14.3"
+  echo "create_eset v0.14.4"
  echo ""
  echo "Arguments:"
  echo "    --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_eset v0.14.3"
+            echo "create_eset v0.14.4"
            exit
            ;;
        --pDataFile)
@@ -794,7 +794,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -219,7 +219,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_fdata v0.14.3
+# create_fdata v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:51Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.14.3"
+  echo "create_fdata v0.14.4"
  echo ""
  echo "Create a fdata file"
  echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_fdata v0.14.3"
+            echo "create_fdata v0.14.4"
            exit
            ;;
        --gtf)
@@ -756,7 +756,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -233,7 +233,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_pdata v0.14.3
+# create_pdata v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:51Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.14.3"
+  echo "create_pdata v0.14.4"
  echo ""
  echo "Create a pdata file by combining the mapping statistics"
  echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_pdata v0.14.3"
+            echo "create_pdata v0.14.4"
            exit
            ;;
        --star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -191,7 +191,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# check_eset v0.14.3
+# check_eset v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:52Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.14.3"
+  echo "check_eset v0.14.4"
  echo ""
  echo "This component test the ExpressionSet object as output by the main pipeline."
  echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_eset v0.14.3"
+            echo "check_eset v0.14.4"
            exit
            ;;
        --eset)
@@ -754,7 +754,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -200,7 +200,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# check_cutadapt_output v0.14.3
+# check_cutadapt_output v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:51Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

 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 v0.14.3"
+  echo "check_cutadapt_output v0.14.4"
  echo ""
  echo "This component test the cutadapt output from the well_demultiplex subworkflow."
  echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_cutadapt_output v0.14.3"
+            echo "check_cutadapt_output v0.14.4"
            exit
            ;;
        --fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -175,7 +175,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish_fastqs v0.14.3
+# publish_fastqs v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.14.3"
+  echo "publish_fastqs v0.14.4"
  echo ""
  echo "Publish the fastq files per well"
  echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_fastqs v0.14.3"
+            echo "publish_fastqs v0.14.4"
            exit
            ;;
        --input)
@@ -750,7 +750,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -315,7 +315,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish_results v0.14.3
+# publish_results v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.14.3"
+  echo "publish_results v0.14.4"
  echo ""
  echo "Publish the results"
  echo ""
@@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_results v0.14.3"
+            echo "publish_results v0.14.4"
            exit
            ;;
        --star_output)
@@ -986,7 +986,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -321,7 +321,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/executable/parallel_map/_viash.yaml
+++ b/target/executable/parallel_map/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# parallel_map v0.14.3
+# parallel_map v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:52Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.14.3"
+  echo "parallel_map v0.14.4"
  echo ""
  echo "Map wells in batch, using STAR"
  echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "parallel_map v0.14.3"
+            echo "parallel_map v0.14.4"
            exit
            ;;
        --input_r1)
@@ -907,7 +907,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -40,6 +40,15 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
+  - type: "file"
+    name: "--preproc_params"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
  - type: "file"
    name: "--output_report"
    info: null
@@ -159,7 +168,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.3"
+  target_tag: "v0.14.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -189,6 +198,7 @@ engines:
    - "DT"
    - "logger"
    - "bit64"
+    - "yaml"
    bioc:
    - "Biobase"
    - "ComplexHeatmap"
@@ -215,11 +225,11 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.4"
-  git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  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\
@@ -251,7 +261,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_report v0.14.3
+# create_report v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -460,15 +460,15 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
  Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
  Rscript -e 'options(warn = 2); if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
  Rscript -e 'options(warn = 2); if (!requireNamespace("ComplexHeatmap", quietly = TRUE)) BiocManager::install("ComplexHeatmap")' && \
-  Rscript -e 'options(warn = 2); remotes::install_cran(c("ggplot2", "knitr", "gridExtra", "RColorBrewer", "processx", "whisker", "rmarkdown", "bookdown", "data.table", "platetools", "htmltools", "DT", "logger", "bit64"), repos = "https://cran.rstudio.com")' && \
+  Rscript -e 'options(warn = 2); remotes::install_cran(c("ggplot2", "knitr", "gridExtra", "RColorBrewer", "processx", "whisker", "rmarkdown", "bookdown", "data.table", "platetools", "htmltools", "DT", "logger", "bit64", "yaml"), repos = "https://cran.rstudio.com")' && \
  Rscript -e 'options(warn = 2); install.packages("oaStyle", repos = c(rdepot = "https://repos.openanalytics.eu/repo/public", getOption("repos")))'

 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="2025-12-03T14:02:50Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.14.3"
+  echo "create_report v0.14.4"
  echo ""
  echo "Create a basic QC report in HTML format based on a number of esets."
  echo ""
@@ -593,6 +593,9 @@ function ViashHelp {
  echo "    --eset"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo ""
+  echo "    --preproc_params"
+  echo "        type: file, file must exist"
+  echo ""
  echo "    --output_report"
  echo "        type: file, required parameter, output, file must exist"
  echo "        example: report.html"
@@ -644,7 +647,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_report v0.14.3"
+            echo "create_report v0.14.4"
            exit
            ;;
        --eset)
@@ -664,6 +667,17 @@ while [[ $# -gt 0 ]]; do
            fi
            shift 1
            ;;
+        --preproc_params)
+            [ -n "$VIASH_PAR_PREPROC_PARAMS" ] && ViashError Bad arguments for option \'--preproc_params\': \'$VIASH_PAR_PREPROC_PARAMS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_PREPROC_PARAMS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --preproc_params. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --preproc_params=*)
+            [ -n "$VIASH_PAR_PREPROC_PARAMS" ] && ViashError Bad arguments for option \'--preproc_params=*\': \'$VIASH_PAR_PREPROC_PARAMS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_PREPROC_PARAMS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --output_report)
            [ -n "$VIASH_PAR_OUTPUT_REPORT" ] && ViashError Bad arguments for option \'--output_report\': \'$VIASH_PAR_OUTPUT_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_REPORT="$2"
@@ -763,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.4'
  fi

  # print dockerfile
@@ -893,6 +907,10 @@ if [ ! -z "$VIASH_PAR_ESET" ]; then
  done
  set +f
 fi
+if [ ! -z "$VIASH_PAR_PREPROC_PARAMS" ] && [ ! -e "$VIASH_PAR_PREPROC_PARAMS" ]; then
+  ViashError "Input file '$VIASH_PAR_PREPROC_PARAMS' does not exist."
+  exit 1
+fi

 # check whether parameters values are of the right type
 if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -996,6 +1014,10 @@ if [ ! -z "$VIASH_PAR_ESET" ]; then
  done
  VIASH_PAR_ESET=$(IFS=';' ; echo "${VIASH_TEST_ESET[*]}")
 fi
+if [ ! -z "$VIASH_PAR_PREPROC_PARAMS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PREPROC_PARAMS")" )
+  VIASH_PAR_PREPROC_PARAMS=$(ViashDockerAutodetectMount "$VIASH_PAR_PREPROC_PARAMS")
+fi
 if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_REPORT")" )
  VIASH_PAR_OUTPUT_REPORT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_REPORT")
@@ -1075,6 +1097,7 @@ cat > "\$tempscript" << 'VIASHMAIN'

 par <- list(
  "eset" = $( if [ ! -z ${VIASH_PAR_ESET+x} ]; then echo -n "strsplit('"; echo -n "$VIASH_PAR_ESET" | sed "s#['\\]#\\\\&#g"; echo "', split = ';')[[1]]"; else echo NULL; fi ),
+  "preproc_params" = $( if [ ! -z ${VIASH_PAR_PREPROC_PARAMS+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_PREPROC_PARAMS" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "output_report" = $( if [ ! -z ${VIASH_PAR_OUTPUT_REPORT+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTPUT_REPORT" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi )
 )
 meta <- list(
@@ -1121,6 +1144,11 @@ esets_normalized <- lapply(par\$eset, function(eset_path) {
  return(file.path(normalizePath(dirname(eset_path)), basename(eset_path)))
 })

+preproc_params_normalized <- NULL
+if(!is.null(par\$preproc_params)){
+  preproc_params_normalized <- file.path(normalizePath(dirname(par\$preproc_params)), basename(par\$preproc_params))
+}
+
 log_info(paste0(
  "Rendering markdown {template} to HTML ",
  "{par\$output_report} with esets {paste(esets_normalized, collapse = ', ')}"
@@ -1135,6 +1163,7 @@ rmarkdown::render(
  clean = TRUE,
  params = list(
    esets = esets_normalized,
+    preproc_params = preproc_params_normalized,
    outputDir = par\$report_dir
  )
 )
@@ -1163,6 +1192,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
    done
    VIASH_PAR_ESET="$VIASH_TEST_ESET"
  fi
+  if [ ! -z "$VIASH_PAR_PREPROC_PARAMS" ]; then
+    VIASH_PAR_PREPROC_PARAMS=$(ViashDockerStripAutomount "$VIASH_PAR_PREPROC_PARAMS")
+  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ]; then
    VIASH_PAR_OUTPUT_REPORT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_REPORT")
  fi
--- a/target/executable/report/create_report/template.Rmd
+++ b/target/executable/report/create_report/template.Rmd
@@ -11,6 +11,8 @@ params:
  esets:
    - sample1.rds
    - sample2.rds
+  preproc_params:
+    - params.yaml  
 ---

 <!---
@@ -32,9 +34,11 @@ div.main-container {



-```{r params, eval = TRUE, include = FALSE}
+```{r get_params, eval = TRUE, include = FALSE}
 outputDir <- params$outputDir
 esets <- params$esets
+preproc_params_file <- params$preproc_params
+
 ```


@@ -91,6 +95,7 @@ library(knitr)
 library(Biobase)
 library(gridExtra)
 library(RColorBrewer)
+library(yaml)
 ```


@@ -115,6 +120,7 @@ names(esetList) <- unlist(pools)
 # Create qcData
 pDataList <- lapply(esetList, function(eset) data.table(pData(eset)))
 qcData <- rbindlist(pDataList, fill = TRUE)
+qcData[, nMappedReads_per_UMI :=  NumberOfMappedReads/NumberOfUMIs]

 textVars <- "SampleName"
 annotationVar <- "PoolName"
@@ -178,6 +184,30 @@ if (length(Design_levels) == 1) {
 }
 ```

+
+
+```{r versions_and_params, results="asis", eval = !is.null(preproc_params_file)}
+
+preproc_params <- gsub(" ", "", unlist(read_yaml(preproc_params_file)))
+
+cat("# Parameters", "\n\n",
+    "<blockquote>", "\n\n",
+    "**The preprocessing parameters were: ** <br>",
+    "`project id: ", preproc_params["project_id"],"`  \n",
+    "`experiment id: ", preproc_params["experiment_id"],"`  \n",
+    "`run id: ", preproc_params["run_id"],"` \n",
+    "`raw data location: ", preproc_params["input"], "`  \n",
+    "`well barcodes: ", preproc_params["barcodesFasta"],"`  \n",
+    "`genome reference: ", preproc_params["genomeDir"],"`  \n",
+    "`gtf annotation: ", preproc_params["annotation"],"`  \n",
+    "`UMI length: ", preproc_params["umi_length"], "`",
+    "</blockquote>",sep="")
+
+
+```
+
+
+
 # Pool Description

 Per pool within this study, there are several pool layout plots shown, based on the
@@ -420,7 +450,7 @@ ggplot(

 #### Density distribution {.unnumbered}

-```{r density_numberOfUMIs}
+```{r density_numberOfUMIs, fig.width=min(c(14, length(unique(qcData$PoolName))*7)), fig.width=min(c(32, length(unique(qcData$PoolName))*7)),}

 ## Pre-filtering data exploration
 dt_plot <- melt(
@@ -432,7 +462,7 @@ dt_plot <- melt(
 readsDensity_plot <- ggplot(dt_plot, aes(value))
 readsDensity_plot <- readsDensity_plot +
  geom_density(aes(fill = variable), alpha=0.8) +
-  facet_grid(~ PoolName, scales = "free_x", space = "fixed", drop = TRUE) +
+  facet_wrap(~ PoolName, scales = "free_x", space = "fixed", drop = TRUE, ncol = 4) +
  geom_vline(
    xintercept = 5e5,
    linetype = "dashed",
@@ -482,6 +512,9 @@ readsDensity_plot

 ```

+
+
+
 ### Number of Genes {.tabset .unnumbered}

 #### Distribution {.unnumbered}
@@ -601,6 +634,26 @@ ggplot(

 ```

+#### Number of Mapped Reads Per UMI {.unnumbered}
+
+```{r mapping_efficiency_5_plate, fig.height = 7}
+ 
+ ggplot(qcData, aes(x = nMappedReads_per_UMI, y = NumberOfMappedReads, colour = PoolName)) + 
+  geom_point() + 
+  xlab('Number of Mapped Reads per UMI') + ylab("Number of Mapped Reads") +
+  ggtitle('Number of Mapped Reads per UMI vs Number of Mapped Reads') + 
+  theme(strip.text.x = element_text(size = 20),
+        panel.spacing = unit(2, "lines"), 
+        text = element_text(size=10), 
+        axis.text = element_text(angle = 90,size = 15), 
+        plot.title = element_text(size=18), 
+        legend.text = element_text(size=15), 
+        legend.title = element_text(size = 17), 
+        axis.title = element_text(size = 15))
+
+
+```
+
 ### Counting Efficiency {.tabset .unnumbered}

 #### Number of Mapped Reads {.unnumbered}
@@ -647,6 +700,23 @@ ggplot(



+#### Number of Mapped Reads per UMI {.unnumbered}
+
+```{r gene_efficiency_3_plate, fig.height = 7} 
+
+ggplot(qcData, aes(x = nMappedReads_per_UMI, y = NumberOfGenes, colour = PoolName)) + geom_point() + 
+     ylab('Number of Genes') + xlab("Number of Mapped Reads per UMI") + ggtitle('Number of Genes vs Number of Mapped Reads per UMI') + 
+  theme(strip.text.x = element_text(size = 20),
+        panel.spacing = unit(2, "lines"), 
+        text = element_text(size=10), 
+        axis.text = element_text(angle = 90,size = 15), 
+        plot.title = element_text(size=18), 
+        legend.text = element_text(size=15), 
+        legend.title = element_text(size = 17), 
+        axis.title = element_text(size = 15))
+
+
+```
 ## Sequencing Saturation {.tabset}

 The barplots below represent the sequencing saturation per sample as determined by STAR, split per pool. 
--- 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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -240,7 +240,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# combine_star_logs v0.14.3
+# combine_star_logs v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:50Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

 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 v0.14.3"
+  echo "combine_star_logs v0.14.4"
  echo ""
  echo "Arguments:"
  echo "    --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "combine_star_logs v0.14.3"
+            echo "combine_star_logs v0.14.4"
            exit
            ;;
        --barcodes)
@@ -825,7 +825,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -224,7 +224,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# generate_pool_statistics v0.14.3
+# generate_pool_statistics v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:52Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

 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 v0.14.3"
+  echo "generate_pool_statistics v0.14.4"
  echo ""
  echo "Arguments:"
  echo "    --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_pool_statistics v0.14.3"
+            echo "generate_pool_statistics v0.14.4"
            exit
            ;;
        --nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -296,7 +296,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# generate_well_statistics v0.14.3
+# generate_well_statistics v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:52Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

 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 v0.14.3"
+  echo "generate_well_statistics v0.14.4"
  echo ""
  echo "Generate summary statistics from BAM files generated by STAR solo."
  echo ""
@@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_well_statistics v0.14.3"
+            echo "generate_well_statistics v0.14.4"
            exit
            ;;
        --input)
@@ -861,7 +861,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  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\
@@ -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 := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# save_params v0.14.3
+# save_params v0.14.4
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-12-03T14:02:51Z"
+LABEL org.opencontainers.image.created="2025-12-12T13:48:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25"
-LABEL org.opencontainers.image.version="v0.14.3"
+LABEL org.opencontainers.image.revision="2a509fa7ae74164a26ec1c2db7e1841410cd985e"
+LABEL org.opencontainers.image.version="v0.14.4"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "save_params v0.14.3"
+  echo "save_params v0.14.4"
  echo ""
  echo "Save parameters to a YAML file"
  echo ""
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "save_params v0.14.3"
+            echo "save_params v0.14.4"
            exit
            ;;
        --id)
@@ -763,7 +763,7 @@ if [[ "$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:v0.14.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -242,7 +242,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -1,4 +1,4 @@
-// create_eset v0.14.3
+// create_eset v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_eset",
  "namespace" : "eset",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3271,7 +3271,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3309,12 +3309,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3332,7 +3332,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4207,7 +4207,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -219,7 +219,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -1,4 +1,4 @@
-// create_fdata v0.14.3
+// create_fdata v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_fdata",
  "namespace" : "eset",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3279,12 +3279,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3302,7 +3302,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -233,7 +233,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -1,4 +1,4 @@
-// create_pdata v0.14.3
+// create_pdata v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_pdata",
  "namespace" : "eset",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3252,7 +3252,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3293,12 +3293,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3316,7 +3316,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3812,7 +3812,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -191,7 +191,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -1,4 +1,4 @@
-// check_eset v0.14.3
+// check_eset v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "check_eset",
  "namespace" : "integration_test_components/htrnaseq",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "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" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3233,12 +3233,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3256,7 +3256,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3906,7 +3906,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -200,7 +200,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -1,4 +1,4 @@
-// check_cutadapt_output v0.14.3
+// check_cutadapt_output v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "check_cutadapt_output",
  "namespace" : "integration_test_components/well_demultiplexing",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3213,7 +3213,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3244,12 +3244,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3267,7 +3267,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "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" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -175,7 +175,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -1,4 +1,4 @@
-// publish_fastqs v0.14.3
+// publish_fastqs v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish_fastqs",
  "namespace" : "io",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3184,7 +3184,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3207,12 +3207,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3230,7 +3230,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3682,7 +3682,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -315,7 +315,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -1,4 +1,4 @@
-// publish_results v0.14.3
+// publish_results v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish_results",
  "namespace" : "io",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3346,7 +3346,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3369,12 +3369,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3392,7 +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 := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3909,7 +3909,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -321,7 +321,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  keywords:
  - "bioinformatics"
  - "sequencing"
--- a/target/nextflow/parallel_map/_viash.yaml
+++ b/target/nextflow/parallel_map/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -1,4 +1,4 @@
-// parallel_map v0.14.3
+// parallel_map v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "parallel_map",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3332,7 +3332,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3379,12 +3379,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3402,7 +3402,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4173,7 +4173,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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: "v0.14.3"
+version: "v0.14.4"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -40,6 +40,15 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
+  - type: "file"
+    name: "--preproc_params"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
  - type: "file"
    name: "--output_report"
    info: null
@@ -159,7 +168,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.3"
+  target_tag: "v0.14.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -189,6 +198,7 @@ engines:
    - "DT"
    - "logger"
    - "bit64"
+    - "yaml"
    bioc:
    - "Biobase"
    - "ComplexHeatmap"
@@ -215,11 +225,11 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.4"
-  git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  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\
@@ -251,7 +261,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -1,4 +1,4 @@
-// create_report v0.14.3
+// create_report v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_report",
  "namespace" : "report",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3095,6 +3095,16 @@ meta = [
          "multiple" : true,
          "multiple_sep" : ";"
        },
+        {
+          "type" : "file",
+          "name" : "--preproc_params",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
        {
          "type" : "file",
          "name" : "--output_report",
@@ -3251,7 +3261,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3287,7 +3297,8 @@ meta = [
            "htmltools",
            "DT",
            "logger",
-            "bit64"
+            "bit64",
+            "yaml"
          ],
          "bioc" : [
            "Biobase",
@@ -3323,12 +3334,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "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" : {
@@ -3346,7 +3357,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3384,6 +3395,7 @@ cat > "$tempscript" << VIASHMAIN

 par <- list(
  "eset" = $( if [ ! -z ${VIASH_PAR_ESET+x} ]; then echo -n "strsplit('"; echo -n "$VIASH_PAR_ESET" | sed "s#['\\\\]#\\\\\\\\&#g"; echo "', split = ';')[[1]]"; else echo NULL; fi ),
+  "preproc_params" = $( if [ ! -z ${VIASH_PAR_PREPROC_PARAMS+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_PREPROC_PARAMS" | sed "s#['\\\\]#\\\\\\\\&#g"; echo "'"; else echo NULL; fi ),
  "output_report" = $( if [ ! -z ${VIASH_PAR_OUTPUT_REPORT+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTPUT_REPORT" | sed "s#['\\\\]#\\\\\\\\&#g"; echo "'"; else echo NULL; fi )
 )
 meta <- list(
@@ -3430,6 +3442,11 @@ esets_normalized <- lapply(par\\$eset, function(eset_path) {
  return(file.path(normalizePath(dirname(eset_path)), basename(eset_path)))
 })

+preproc_params_normalized <- NULL
+if(!is.null(par\\$preproc_params)){
+  preproc_params_normalized <- file.path(normalizePath(dirname(par\\$preproc_params)), basename(par\\$preproc_params))
+}
+
 log_info(paste0(
  "Rendering markdown {template} to HTML ",
  "{par\\$output_report} with esets {paste(esets_normalized, collapse = ', ')}"
@@ -3444,6 +3461,7 @@ rmarkdown::render(
  clean = TRUE,
  params = list(
    esets = esets_normalized,
+    preproc_params = preproc_params_normalized,
    outputDir = par\\$report_dir
  )
 )
@@ -3831,7 +3849,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/report/create_report",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "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 = 'v0.14.3'
+  version = 'v0.14.4'
  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/report/create_report/nextflow_schema.json
+++ b/target/nextflow/report/create_report/nextflow_schema.json
@@ -19,6 +19,12 @@
          "description": "",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
+        "preproc_params": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
+        },
        "output_report": {
          "type": "string",
          "format": "path",
--- a/target/nextflow/report/create_report/template.Rmd
+++ b/target/nextflow/report/create_report/template.Rmd
@@ -11,6 +11,8 @@ params:
  esets:
    - sample1.rds
    - sample2.rds
+  preproc_params:
+    - params.yaml  
 ---

 <!---
@@ -32,9 +34,11 @@ div.main-container {



-```{r params, eval = TRUE, include = FALSE}
+```{r get_params, eval = TRUE, include = FALSE}
 outputDir <- params$outputDir
 esets <- params$esets
+preproc_params_file <- params$preproc_params
+
 ```


@@ -91,6 +95,7 @@ library(knitr)
 library(Biobase)
 library(gridExtra)
 library(RColorBrewer)
+library(yaml)
 ```


@@ -115,6 +120,7 @@ names(esetList) <- unlist(pools)
 # Create qcData
 pDataList <- lapply(esetList, function(eset) data.table(pData(eset)))
 qcData <- rbindlist(pDataList, fill = TRUE)
+qcData[, nMappedReads_per_UMI :=  NumberOfMappedReads/NumberOfUMIs]

 textVars <- "SampleName"
 annotationVar <- "PoolName"
@@ -178,6 +184,30 @@ if (length(Design_levels) == 1) {
 }
 ```

+
+
+```{r versions_and_params, results="asis", eval = !is.null(preproc_params_file)}
+
+preproc_params <- gsub(" ", "", unlist(read_yaml(preproc_params_file)))
+
+cat("# Parameters", "\n\n",
+    "<blockquote>", "\n\n",
+    "**The preprocessing parameters were: ** <br>",
+    "`project id: ", preproc_params["project_id"],"`  \n",
+    "`experiment id: ", preproc_params["experiment_id"],"`  \n",
+    "`run id: ", preproc_params["run_id"],"` \n",
+    "`raw data location: ", preproc_params["input"], "`  \n",
+    "`well barcodes: ", preproc_params["barcodesFasta"],"`  \n",
+    "`genome reference: ", preproc_params["genomeDir"],"`  \n",
+    "`gtf annotation: ", preproc_params["annotation"],"`  \n",
+    "`UMI length: ", preproc_params["umi_length"], "`",
+    "</blockquote>",sep="")
+
+
+```
+
+
+
 # Pool Description

 Per pool within this study, there are several pool layout plots shown, based on the
@@ -420,7 +450,7 @@ ggplot(

 #### Density distribution {.unnumbered}

-```{r density_numberOfUMIs}
+```{r density_numberOfUMIs, fig.width=min(c(14, length(unique(qcData$PoolName))*7)), fig.width=min(c(32, length(unique(qcData$PoolName))*7)),}

 ## Pre-filtering data exploration
 dt_plot <- melt(
@@ -432,7 +462,7 @@ dt_plot <- melt(
 readsDensity_plot <- ggplot(dt_plot, aes(value))
 readsDensity_plot <- readsDensity_plot +
  geom_density(aes(fill = variable), alpha=0.8) +
-  facet_grid(~ PoolName, scales = "free_x", space = "fixed", drop = TRUE) +
+  facet_wrap(~ PoolName, scales = "free_x", space = "fixed", drop = TRUE, ncol = 4) +
  geom_vline(
    xintercept = 5e5,
    linetype = "dashed",
@@ -482,6 +512,9 @@ readsDensity_plot

 ```

+
+
+
 ### Number of Genes {.tabset .unnumbered}

 #### Distribution {.unnumbered}
@@ -601,6 +634,26 @@ ggplot(

 ```

+#### Number of Mapped Reads Per UMI {.unnumbered}
+
+```{r mapping_efficiency_5_plate, fig.height = 7}
+ 
+ ggplot(qcData, aes(x = nMappedReads_per_UMI, y = NumberOfMappedReads, colour = PoolName)) + 
+  geom_point() + 
+  xlab('Number of Mapped Reads per UMI') + ylab("Number of Mapped Reads") +
+  ggtitle('Number of Mapped Reads per UMI vs Number of Mapped Reads') + 
+  theme(strip.text.x = element_text(size = 20),
+        panel.spacing = unit(2, "lines"), 
+        text = element_text(size=10), 
+        axis.text = element_text(angle = 90,size = 15), 
+        plot.title = element_text(size=18), 
+        legend.text = element_text(size=15), 
+        legend.title = element_text(size = 17), 
+        axis.title = element_text(size = 15))
+
+
+```
+
 ### Counting Efficiency {.tabset .unnumbered}

 #### Number of Mapped Reads {.unnumbered}
@@ -647,6 +700,23 @@ ggplot(



+#### Number of Mapped Reads per UMI {.unnumbered}
+
+```{r gene_efficiency_3_plate, fig.height = 7} 
+
+ggplot(qcData, aes(x = nMappedReads_per_UMI, y = NumberOfGenes, colour = PoolName)) + geom_point() + 
+     ylab('Number of Genes') + xlab("Number of Mapped Reads per UMI") + ggtitle('Number of Genes vs Number of Mapped Reads per UMI') + 
+  theme(strip.text.x = element_text(size = 20),
+        panel.spacing = unit(2, "lines"), 
+        text = element_text(size=10), 
+        axis.text = element_text(angle = 90,size = 15), 
+        plot.title = element_text(size=18), 
+        legend.text = element_text(size=15), 
+        legend.title = element_text(size = 17), 
+        axis.title = element_text(size = 15))
+
+
+```
 ## Sequencing Saturation {.tabset}

 The barplots below represent the sequencing saturation per sample as determined by STAR, split per pool. 
--- 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: "v0.14.3"
+version: "v0.14.4"
 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: "v0.14.3"
+  target_tag: "v0.14.4"
  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: "e9507042c57fcbf9a03d769d758d5d36e1631d25"
+  git_commit: "2a509fa7ae74164a26ec1c2db7e1841410cd985e"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.14.3"
+  version: "v0.14.4"
  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
  description: "This workflow is designed to process high-throughput RNA-seq data,\
    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -240,7 +240,7 @@ package_config:
    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
  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: v0.14.3
+version: v0.14.4
 summary: |
  A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -1,4 +1,4 @@
-// combine_star_logs v0.14.3
+// combine_star_logs v0.14.4
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_star_logs",
  "namespace" : "stats",
-  "version" : "v0.14.3",
+  "version" : "v0.14.4",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3254,7 +3254,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.3",
+      "target_tag" : "v0.14.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3295,12 +3295,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.4",
-    "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25",
+    "git_commit" : "2a509fa7ae74164a26ec1c2db7e1841410cd985e",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.14.3",
+    "version" : "v0.14.4",
    "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
    "info" : {
@@ -3318,7 +3318,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3977,7 +3977,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/combine_star_logs",
-    "tag" : "v0.14.3"
+    "tag" : "v0.14.4"
  },
  "tag" : "$id"
 }'''),
--- a/Show More
+++ b/Show More