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

Build pipeline: viash-hub.htrnaseq.v0.14.7-lr47z

Source commit: 07ba686a46

Source message: Bump version to v0.14.7

.gitignore

@@ -14,6 +14,7 @@ work
 # R related files
 .Rproj.user
 htrnaseq.Rproj
+.Rhistory
 
 # vscode
 .vscode

CHANGELOG.md

@@ -1,22 +1,64 @@
-# htrnaseq v0.14.1
+# htrnaseq v0.14.7
+
+## Bug fixes
+
+* Revert breaking changes from PR #95 and re-implement writing (sub-)workflow version to a separate file (PR #103).
+
+# htrnaseq v0.14.6
+
+## Minor changes
+
+* Update `utils/save_params` to capture sub-workflow names and versions alongside input parameters (PR #95).
+
+# htrnaseq v0.14.5
+
+## Bug fixes
+
+`create_eset`: raise an error when the output eset is empty (PR #98).
+
+# 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
+
+* `parallel_map`: detection of gzip compressed files now works if the file inadvertently also matches another file type (PR #94).
 
 # Minor changes
 
+* Change `cutadapt`'s memory label from `highmem` to `midmem` (PR #93).
+
+# htrnaseq v0.14.2
+
+## Bug fixes
+
+* Fix esets not being created when processing multiple samples from a single run (PR #92).
+
+* Publishing a very small amount of data no longer throws an error (calling `dropRight` on a `null` object) (PR #92). 
+
+# htrnaseq v0.14.1
+
+## Minor changes
+
 * FASTQ files are now gzip compressed (PR #88).
 
 * Bump biobox to `v0.4.2` and craftbox to `v0.3.1` (PR #88).
 
-# Bug fixes
+## Bug fixes
 
 * Fix an issue where samples with the same experiment ID but from different projects were concatenated (PR #87). 
 
 # htrnaseq v0.14.0
 
-# Major changes
+## Major changes
 
 * `runner`: major refactor that allows sequencing runs to be only demultiplexed once (PR #85).
 
-# Minor changes
+## Minor changes
 
 * `generate_well_statistics`: increase memory requirements from `verylowmem` to `lowmem` (PR #86).
 

_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

src/eset/create_eset/script.R

@@ -378,6 +378,16 @@ create_eset <- function(feature_annotation_path,
                                   annotation = additional_info)
 
   eset <- eset[, colSums(exprs(eset)) != 0]
+
+  if (nrow(eset) == 0) {
+    stop("Count matrix does not seem to contain any features.")
+  }
+
+  if (ncol(eset) == 0) {
+    stop("Count matrix does not seem to contain any samples.")
+  }
+
+
   saveRDS(eset, file = output_path)
 
   message(paste0("eset created succesfully for ", ncol(eset),

src/io/publish_results/code.sh

@@ -19,6 +19,7 @@ declare -A path_pars_dirs=(
 declare -A path_pars_files=(
   ["par_html_report_output"]="par_html_report"
   ["par_run_params_output"]="par_run_params"
+  ["par_run_metadata_output"]="par_run_metadata"
 )
 
 echo "Canonicalizing output paths."

src/io/publish_results/config.vsh.yaml

@@ -35,6 +35,9 @@ argument_groups:
       - name: "--run_params"
         type: file
         required: true
+      - name: "--run_metadata"
+        type: file
+        required: true
   - name: Output directory
     description: |
       Determines the name of output directories
@@ -69,6 +72,9 @@ argument_groups:
       - name: "--run_params_output"
         type: file
         direction: output
+      - name: "--run_metadata_output"
+        type: file
+        direction: output
       - name: "--html_report_output"
         type: file
         direction: output

src/parallel_map/script.sh

@@ -169,7 +169,9 @@ function _run() {
 
   function is_gzipped {
     printf "Checking if input '$1' (barcode '$barcode') is gzipped... "
-    if file "$1" | grep -q 'gzip'; then
+    # The file might match more than one mime-type, but if the `-k` flag is not
+    # set, file will only output one. 
+    if file --mime-type -k "$1" | grep -q 'gzip'; then
       echo "Done, detected compressed file."
       return
     fi

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

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
   )
 )

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. 

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"
 ))
 

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

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}
       )

src/workflows/runner/config.vsh.yaml

@@ -73,6 +73,12 @@ argument_groups:
         type: file
         direction: output
         default: params.yaml
+      - name: "--run_metadata"
+        type: file
+        description: |
+          YAML file containing meta information about the file — .e.g. versions of (sub)-workflows.
+        direction: output
+        default: metadata.yaml
       - name: "--star_output_dir"
         type: file
         direction: output

src/workflows/runner/integration_test.sh

@@ -37,4 +37,12 @@ nextflow \
   -config ./src/config/labels.config \
   -entry test_same_experiment_id_different_projects_wf \
   -resume \
+  -profile docker,local
+
+nextflow \
+  run . \
+  -main-script src/workflows/runner/test.nf \
+  -config ./src/config/labels.config \
+  -entry test_multiple_samples \
+  -resume \
   -profile docker,local

src/workflows/runner/main.nf

@@ -6,8 +6,6 @@ def date = new Date().format('yyyyMMdd_hhmmss')
 session = nextflow.Nextflow.getSession()
 final service = session.publishDirExecutorService()
 
-
-
 def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
@@ -21,6 +19,36 @@ def regex_trailing_slashes = ~/\/+$/
 def results_publish_dir = params.results_publish_dir - regex_trailing_slashes
 def fastq_publish_dir = params.fastq_publish_dir - regex_trailing_slashes
 
+def get_workflow_analysis() {
+  def dependencies = []
+  
+  if (meta.config.dependencies) {
+    meta.config.dependencies.each { dep_spec ->
+      def dependency_name = dep_spec.alias ? dep_spec.alias : dep_spec.name
+      def dependency_var = file(dependency_name).name
+      def dependency = binding.getVariable(dependency_var)
+        
+      def dep_entry = new LinkedHashMap()
+      dep_entry.name = dependency.config.name ?: "unknown_name"
+      dep_entry.version = dependency.config.version ?: "unknown_version"
+      dependencies << dep_entry
+    }
+  }
+  
+  // Build main analysis entry with dependencies using LinkedHashMap for order
+  def main_entry = [
+    "name": meta.config.name ?: "unknown_name",
+    "version": meta.config.version ?: "unknown_version",
+    "dependencies": dependencies
+  ]
+  
+  def analysis = ["versions": [main_entry]]
+  
+  println("Analysis workflows: ${analysis}")
+  return analysis
+}
+
+
 
 /* 
 This is a utility workflow that gathers the input events and saves their state to a YAML file.
@@ -38,7 +66,15 @@ workflow save_params_wf {
         def all_states = states.collect{it[1]}
         def run_params_output_templates = all_states.collect{it.run_params}
         assert run_params_output_templates.unique().size() == 1: "The value for the 'run_params' parameter is not the same across runs."
-        def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states]
+
+        def run_metadata_output_templates = all_states.collect{it.run_metadata}
+        assert run_metadata_output_templates.unique().size() == 1: "The value for the 'run_metadata' parameter is not the same across runs."
+
+        def new_state = [
+          "run_params": run_params_output_templates[0],
+          "run_metadata": run_metadata_output_templates[0],
+          "all_states": all_states
+        ]
         return [new_id, new_state]
       }
       | save_params.run(
@@ -72,6 +108,23 @@ workflow save_params_wf {
         },
         toState: ["run_params": "output"]
       )
+      | save_params.run(
+        key: "save_meta_runner",
+        fromState: {id, state ->
+          def yaml_builder = new org.yaml.snakeyaml.Yaml()
+          def analysis_yaml = yaml_builder.dump(get_workflow_analysis())
+          def encoded_analysis = analysis_yaml.bytes.encodeBase64().toString()
+          return [
+            "id": id,
+            "params_yaml": encoded_analysis,
+            "output": state.run_metadata,
+          ]
+        },
+        toState: { id, output, state ->
+          state + [ run_metadata: output.output ]
+        }
+      )
+
 
   emit:
   output_ch
@@ -243,7 +296,7 @@ workflow run_wf {
     This will cause the the `well_fastqs_to_esets` workflow to do the grouping and concatenation of the 
     events with the same sample ID.
     */
-    htrnaseq_ch = demultiplex_ch
+    demultiplex_with_input_ids_ch = demultiplex_ch
       // The IDs in the demultiplex_ch are of format '<run_id>/<sample_id>' (not split per experiment.)
       | flatMap {id, state ->
         state.event_ids.collect{ event_id ->
@@ -252,8 +305,12 @@ workflow run_wf {
         }
       }
       // The event IDs at this point are the same IDs in the `input_ch` in order to do the join
-      | join(input_ch)
-      | map {event_id, demux_state, input_state ->
+
+    htrnaseq_ch = input_ch
+      | cross(demultiplex_with_input_ids_ch)
+      | map {input_event, demux_event  ->
+        def (event_id, demux_state) = demux_event
+        def input_state = input_event[1] 
         def keys_to_transfer = [
           "umi_length",
           "annotation",
@@ -267,7 +324,8 @@ workflow run_wf {
           "eset_dir",
           "f_data_dir",
           "p_data_dir",
-          "run_params"
+          "run_params",
+          "run_metadata"
         ]
         def new_state = demux_state + input_state.subMap(keys_to_transfer)
 
@@ -278,7 +336,8 @@ workflow run_wf {
           "eset_dir",
           "f_data_dir",
           "p_data_dir",
-          "run_params"
+          "run_params",
+          "run_metadata"
         ]
         new_state = new_state.collectEntries{k, v ->
           def newKey = keys_to_rename.contains(k) ? "${k}_workflow" : k
@@ -364,7 +423,10 @@ workflow run_wf {
       // Add the run parameter YAML to the output
       | map {id, grouped_ch_state, _, save_params_state ->
         assert save_params_state.run_params.isFile()
-        def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
+        def new_state = grouped_ch_state + [
+          "run_params": save_params_state.run_params,
+          "run_metadata": save_params_state.run_metadata
+        ]
         return [id, new_state]
       }
       // Group the events in order to publish the results per experiment
@@ -402,8 +464,10 @@ workflow run_wf {
             "f_data_dir_workflow",
             "p_data_dir_workflow",
             "run_params_workflow",
+            "run_metadata_workflow",
             "f_data",
-            "run_params"
+            "run_params",
+            "run_metadata"
           ]
           def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name ->
             argument_values = states.collect{it.get(argument_name)}.unique()
@@ -446,9 +510,11 @@ workflow run_wf {
             p_data: state.p_data,
             html_report: state.html_report,
             run_params: state.run_params,
+            run_metadata: state.run_metadata,
             // Output locations
             html_report_output: "${state.results_prefix}/${state.html_report.name}", 
             run_params_output: "${state.results_prefix}/${state.run_params_workflow}",
+            run_metadata_output: "${state.results_prefix}/${state.run_metadata_workflow}",
             star_output_dir: "${state.results_prefix}/${state.star_output_dir_workflow}",
             nrReadsNrGenesPerChrom_dir: "${state.results_prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}",
             star_qc_metrics_dir: "${state.results_prefix}/${state.star_qc_metrics_dir_workflow}",
@@ -460,6 +526,7 @@ workflow run_wf {
         toState: { id, result, state -> 
           result + [
             "run_params": state.run_params,
+            "run_metadata": state.run_metadata,
             "_meta": ["join_id": state.event_id[0]],
             "results_prefix": state.results_prefix
           ] 
@@ -491,7 +558,7 @@ workflow run_wf {
   awaited_events_ch = results_publish_ch.mix(fastq_publish_ch)
     | toSortedList()
     | map {states ->
-      if (states.size == 0) {
+      if (states.size() == 0) {
         has_published.compareAndSet(false, true)
         error("There seems to be nothing to publish!")
       }
@@ -503,6 +570,12 @@ workflow run_wf {
     // Create periodic events in order to check for the publishing to be done
     | combine(interval_at_least_one_event_ch)
     | until { event ->
+      // Prevent until to output nothing by stopping on the first item of the channel.
+      // It will output 'null' when its the first iteration.
+      // This happens when there is not a lot of data to publish and/or the transfer is fast.
+      if (event[-1] == 0) {
+        return false
+      }
       println("Checking if publishing has finished in service ${service}")
       def running_tasks = null
       if(service instanceof ThreadPoolExecutor) {
@@ -558,6 +631,7 @@ workflow run_wf {
         "f_data_dir",
         "p_data_dir",
         "run_params",
+        "run_metadata",
         "_meta"
       ]
     )

src/workflows/runner/test.nf

@@ -694,3 +694,136 @@ workflow test_same_experiment_id_different_projects_wf {
         }
     }
 }
+
+
+
+workflow test_multiple_samples {
+  
+  /*
+  Test a sequencing run with multiple samples
+  */
+
+  pipeline_version = get_version(viash_config)
+  resources_test = file(params.resources_test)
+
+  // results_publish_dir and results_publish_dir are inherited using params
+  // but they must be defined in the state as well because viash will check
+  // if all arguments are present in the hashmap
+  output_ch = Channel.fromList([
+    [
+        id: "run_1_exp_bar",
+        run_id: "run_1",
+        input: resources_test.resolve("10k_multiple_samples/SRR14730301_SRR14730302"),
+        genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
+        barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
+        annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
+        project_id: "foo",
+        experiment_id: "bar",
+        fastq_publish_dir: params.fastq_publish_dir,
+        results_publish_dir: params.results_publish_dir,
+    ],
+  ])
+  | map { state -> [state.id, state]}
+  | runner.run(
+    toState: { id, output, state -> output + [orig_input: state.input] }
+  )
+  | view { output ->
+    assert output.size() == 2 : "outputs should contain two elements; [id, file]"
+    "Output: $output"
+  }
+
+  tosortedlistch = output_ch
+    | toSortedList()
+    | map {events ->
+        assert events.size() == 1, "Expected 2 events to be output, found ${events.size()}"
+        events
+    }
+    | map {states -> 
+        def output_state = states.find{id, _ -> id == "foo/bar"}[1]
+        assert output_state.eset_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.rds", "VH02001614.rds"].toSet()
+        assert output_state.star_output_dir.listFiles().collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
+        ["VH02001612", "VH02001614"].each{it ->
+           assert output_state.star_output_dir.resolve(it).toRealPath().listFiles().collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+        }
+        assert output_state.star_qc_metrics_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
+        assert output_state.nrReadsNrGenesPerChrom_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
+        assert output_state.run_params.isFile()
+    }
+
+
+    workflow.onComplete = {
+        try {
+            // Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
+            // So in order for the assert statement to work (or allow other errors to let the tests to fail)
+            // We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
+            // The error message will show up in .nextflow.log
+            def fastq_subdir = file("${params.fastq_publish_dir}")
+            assert fastq_subdir.isDirectory()
+            def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
+            def expected_run_folders = ["run_1"].toSet()
+            assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
+            unique_dirs = [
+                "run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
+            ]
+            assert unique_dirs.every{it.value.size() == 1}
+            unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
+
+            assert unique_dirs.every{it.value.isDirectory()}
+            assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
+            def expected_samples = [
+                "run1": ["VH02001612", "VH02001614"]
+            ]
+
+            unique_dirs.each{_key, _value ->
+                def samples = expected_samples[_key]
+                samples.each {expected_sample ->
+                    def expected_sample_dir = _value.resolve(expected_sample)
+                    assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
+                    def expected_fastq_files = [
+                        "A1_R1_001.fastq.gz", "A1_R2_001.fastq.gz", 
+                        "B1_R1_001.fastq.gz", "B1_R2_001.fastq.gz",
+                        "unknown_R1_001.fastq.gz", "unknown_R2_001.fastq.gz"]
+                    def found_files = files("${expected_sample_dir}/*.fastq.gz", type: 'any')
+                    assert found_files.every{it.isFile()}
+                    assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
+                }
+            }
+
+            // Experiment foo/bar
+            def results_subdir = file("${params.results_publish_dir}")
+            assert fastq_subdir.isDirectory()
+            def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
+            assert expected_subdir.isDirectory()
+            def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
+            assert expected_result_dir.size() == 1
+            expected_result_dir = expected_result_dir[0]
+            assert expected_result_dir.isDirectory()
+            def expected_esets = ["VH02001612.rds", "VH02001614.rds"]
+            def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
+            assert found_esets.size() == 2
+            assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
+            expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"]
+            def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
+            assert found_pdata.size() == 2
+            assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
+            def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
+            assert found_nr_genes_nr_reads.size() == 2
+            assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet() 
+            def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
+            assert found_star_logs.size() == 2
+            assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
+            def star_output = file("${expected_result_dir}/star_output", type: 'any')
+            assert star_output.isDirectory()
+            
+            assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
+            assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+            assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+            assert file("${expected_result_dir}/report.html").isFile()
+            assert file("${expected_result_dir}/params.yaml").isFile()
+            assert file("${expected_result_dir}/fData/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
+
+        } catch (Exception e) {
+            throw new WorkflowScriptErrorException("Integration test failed!", e)
+        }
+    }
+}

src/workflows/well_demultiplex/main.nf

@@ -51,7 +51,7 @@ workflow run_wf {
         }
       }
       | cutadapt.run(
-        directives: [label: ["highmem", "midcpu"]],
+        directives: [label: ["midmem", "midcpu"]],
         fromState: { id, state ->
           [
             input: state.input_r1,

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

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",
       ])
 

target/_private/nextflow/utils/listInputDir/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "listInputDir"
 namespace: "utils"
-version: "v0.14.1"
+version: "v0.14.7"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -169,11 +169,11 @@ build_info:
   output: "target/_private/nextflow/utils/listInputDir"
   executable: "target/_private/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -193,7 +193,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -205,7 +205,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/_private/nextflow/utils/listInputDir/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/_private/nextflow/utils/listInputDir/main.nf

@@ -1,4 +1,4 @@
-// listInputDir v0.14.1
+// listInputDir v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "listInputDir",
   "namespace" : "utils",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3236,18 +3236,18 @@ meta = [
     "engine" : "native|native",
     "output" : "target/_private/nextflow/utils/listInputDir",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3259,7 +3259,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",

target/_private/nextflow/utils/listInputDir/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'utils/listInputDir'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'List the contents of a directory and parse contained fastq files'
 }
 

target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "well_fastqs_to_esets"
 namespace: "workflows"
-version: "v0.14.1"
+version: "v0.14.7"
 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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   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: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -350,7 +360,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -362,7 +372,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf

@@ -1,4 +1,4 @@
-// well_fastqs_to_esets v0.14.1
+// well_fastqs_to_esets v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "well_fastqs_to_esets",
   "namespace" : "workflows",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "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" : ";"
         }
       ]
     },
@@ -3444,18 +3455,18 @@ meta = [
     "engine" : "native|native",
     "output" : "target/_private/nextflow/workflows/well_fastqs_to_esets",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -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 := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "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",
       ])
 

target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/well_fastqs_to_esets'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'Map a list of FASTQ files (one for each well) to a reference genome and generate count matrices.\nSometimes counts from different FASTQ files need to be concatenated. This is done bases on the sample_id:\nif the sample ID of the two plates are identical, the FASTQ files will we joined _before_ mapping.\n'
   author = 'Dries Schaumont'
 }

target/executable/eset/create_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -206,11 +206,11 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -230,7 +230,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -242,7 +242,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/eset/create_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/eset/create_eset/create_eset

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_eset v0.14.1
+# create_eset v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:24Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.14.1"
+  echo "create_eset v0.14.7"
   echo ""
   echo "Arguments:"
   echo "    --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_eset v0.14.1"
+            echo "create_eset v0.14.7"
             exit
             ;;
         --pDataFile)
@@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.7'
   fi
 
   # print dockerfile
@@ -1538,6 +1538,16 @@ create_eset <- function(feature_annotation_path,
                                   annotation = additional_info)
 
   eset <- eset[, colSums(exprs(eset)) != 0]
+
+  if (nrow(eset) == 0) {
+    stop("Count matrix does not seem to contain any features.")
+  }
+
+  if (ncol(eset) == 0) {
+    stop("Count matrix does not seem to contain any samples.")
+  }
+
+
   saveRDS(eset, file = output_path)
 
   message(paste0("eset created succesfully for ", ncol(eset),

target/executable/eset/create_fdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -154,7 +154,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -183,11 +183,11 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -207,7 +207,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -219,7 +219,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/eset/create_fdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/eset/create_fdata/create_fdata

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_fdata v0.14.1
+# create_fdata v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:24Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.14.1"
+  echo "create_fdata v0.14.7"
   echo ""
   echo "Create a fdata file"
   echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_fdata v0.14.1"
+            echo "create_fdata v0.14.7"
             exit
             ;;
         --gtf)
@@ -756,7 +756,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.7'
   fi
 
   # print dockerfile

target/executable/eset/create_pdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -168,7 +168,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -197,11 +197,11 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -221,7 +221,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -233,7 +233,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/eset/create_pdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/eset/create_pdata/create_pdata

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_pdata v0.14.1
+# create_pdata v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:24Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.14.1"
+  echo "create_pdata v0.14.7"
   echo ""
   echo "Create a pdata file by combining the mapping statistics"
   echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_pdata v0.14.1"
+            echo "create_pdata v0.14.7"
             exit
             ;;
         --star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.7'
   fi
 
   # print dockerfile

target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -134,7 +134,7 @@ engines:
   id: "docker"
   image: "bioconductor/bioconductor_docker:3.19"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -155,11 +155,11 @@ build_info:
   output: "target/executable/integration_test_components/htrnaseq/check_eset"
   executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -179,7 +179,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -191,7 +191,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/integration_test_components/htrnaseq/check_eset/check_eset

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# check_eset v0.14.1
+# check_eset v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.14.1"
+  echo "check_eset v0.14.7"
   echo ""
   echo "This component test the ExpressionSet object as output by the main pipeline."
   echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_eset v0.14.1"
+            echo "check_eset v0.14.7"
             exit
             ;;
         --eset)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.7'
   fi
 
   # print dockerfile

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,11 +164,11 @@ build_info:
   output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -188,7 +188,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -200,7 +200,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# check_cutadapt_output v0.14.1
+# check_cutadapt_output v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_cutadapt_output v0.14.1"
+  echo "check_cutadapt_output v0.14.7"
   echo ""
   echo "This component test the cutadapt output from the well_demultiplex subworkflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_cutadapt_output v0.14.1"
+            echo "check_cutadapt_output v0.14.7"
             exit
             ;;
         --fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.7'
   fi
 
   # print dockerfile

target/executable/io/publish_fastqs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.14.1"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -139,11 +139,11 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -163,7 +163,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -175,7 +175,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/io/publish_fastqs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/io/publish_fastqs/publish_fastqs

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish_fastqs v0.14.1
+# publish_fastqs v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.14.1"
+  echo "publish_fastqs v0.14.7"
   echo ""
   echo "Publish the fastq files per well"
   echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish_fastqs v0.14.1"
+            echo "publish_fastqs v0.14.7"
             exit
             ;;
         --input)
@@ -750,7 +750,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.7'
   fi
 
   # print dockerfile

target/executable/io/publish_results/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.14.1"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -77,6 +77,15 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output directory"
   description: "Determines the name of output directories\n"
   arguments:
@@ -158,6 +167,15 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata_output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
   - type: "file"
     name: "--html_report_output"
     info: null
@@ -261,7 +279,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -279,11 +297,11 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -303,7 +321,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -315,7 +333,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/io/publish_results/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/io/publish_results/publish_results

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish_results v0.14.1
+# publish_results v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.14.1"
+  echo "publish_results v0.14.7"
   echo ""
   echo "Publish the results"
   echo ""
@@ -600,6 +600,9 @@ function ViashHelp {
   echo "    --run_params"
   echo "        type: file, required parameter, file must exist"
   echo ""
+  echo "    --run_metadata"
+  echo "        type: file, required parameter, file must exist"
+  echo ""
   echo "Output directory:"
   echo "    Determines the name of output directories"
   echo ""
@@ -633,6 +636,9 @@ function ViashHelp {
   echo "    --run_params_output"
   echo "        type: file, output, file must exist"
   echo ""
+  echo "    --run_metadata_output"
+  echo "        type: file, output, file must exist"
+  echo ""
   echo "    --html_report_output"
   echo "        type: file, output, file must exist"
   echo ""
@@ -683,7 +689,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish_results v0.14.1"
+            echo "publish_results v0.14.7"
             exit
             ;;
         --star_output)
@@ -810,6 +816,17 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_RUN_PARAMS=$(ViashRemoveFlags "$1")
             shift 1
             ;;
+        --run_metadata)
+            [ -n "$VIASH_PAR_RUN_METADATA" ] && ViashError Bad arguments for option \'--run_metadata\': \'$VIASH_PAR_RUN_METADATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_metadata. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --run_metadata=*)
+            [ -n "$VIASH_PAR_RUN_METADATA" ] && ViashError Bad arguments for option \'--run_metadata=*\': \'$VIASH_PAR_RUN_METADATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
         --star_output_dir)
             [ -n "$VIASH_PAR_STAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--star_output_dir\': \'$VIASH_PAR_STAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_STAR_OUTPUT_DIR="$2"
@@ -887,6 +904,17 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashRemoveFlags "$1")
             shift 1
             ;;
+        --run_metadata_output)
+            [ -n "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && ViashError Bad arguments for option \'--run_metadata_output\': \'$VIASH_PAR_RUN_METADATA_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA_OUTPUT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_metadata_output. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --run_metadata_output=*)
+            [ -n "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && ViashError Bad arguments for option \'--run_metadata_output=*\': \'$VIASH_PAR_RUN_METADATA_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
         --html_report_output)
             [ -n "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && ViashError Bad arguments for option \'--html_report_output\': \'$VIASH_PAR_HTML_REPORT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_HTML_REPORT_OUTPUT="$2"
@@ -986,7 +1014,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.7'
   fi
 
   # print dockerfile
@@ -1102,6 +1130,10 @@ if [ -z ${VIASH_PAR_RUN_PARAMS+x} ]; then
   ViashError '--run_params' is a required argument. Use "--help" to get more information on the parameters.
   exit 1
 fi
+if [ -z ${VIASH_PAR_RUN_METADATA+x} ]; then
+  ViashError '--run_metadata' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
 if [ -z ${VIASH_META_NAME+x} ]; then
   ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
   exit 1
@@ -1228,6 +1260,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS" ]; then
   ViashError "Input file '$VIASH_PAR_RUN_PARAMS' does not exist."
   exit 1
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA" ] && [ ! -e "$VIASH_PAR_RUN_METADATA" ]; then
+  ViashError "Input file '$VIASH_PAR_RUN_METADATA' does not exist."
+  exit 1
+fi
 
 # check whether parameters values are of the right type
 if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -1325,6 +1361,9 @@ fi
 if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")" ]; then
   mkdir -p "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")"
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_METADATA_OUTPUT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_RUN_METADATA_OUTPUT")"
+fi
 if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")" ]; then
   mkdir -p "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")"
 fi
@@ -1415,6 +1454,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_PARAMS")" )
   VIASH_PAR_RUN_PARAMS=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS")
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_METADATA")" )
+  VIASH_PAR_RUN_METADATA=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_METADATA")
+fi
 if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_OUTPUT_DIR")" )
   VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_OUTPUT_DIR")
@@ -1450,6 +1493,11 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
   VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
   VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_PARAMS_OUTPUT" )
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_METADATA_OUTPUT")" )
+  VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_METADATA_OUTPUT")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_METADATA_OUTPUT" )
+fi
 if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_HTML_REPORT_OUTPUT")" )
   VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_HTML_REPORT_OUTPUT")
@@ -1532,6 +1580,7 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#'
 $( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA+x} ]; then echo "${VIASH_PAR_RUN_METADATA}" | sed "s#'#'\"'\"'#g;s#.*#par_run_metadata='&'#" ; else echo "# par_run_metadata="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi )
@@ -1539,6 +1588,7 @@ $( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed
 $( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_METADATA_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_metadata_output='&'#" ; else echo "# par_run_metadata_output="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
@@ -1581,6 +1631,7 @@ declare -A path_pars_dirs=(
 declare -A path_pars_files=(
   ["par_html_report_output"]="par_html_report"
   ["par_run_params_output"]="par_run_params"
+  ["par_run_metadata_output"]="par_run_metadata"
 )
 
 echo "Canonicalizing output paths."
@@ -1720,6 +1771,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
   if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then
     VIASH_PAR_RUN_PARAMS=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS")
   fi
+  if [ ! -z "$VIASH_PAR_RUN_METADATA" ]; then
+    VIASH_PAR_RUN_METADATA=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_METADATA")
+  fi
   if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
     VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_OUTPUT_DIR")
   fi
@@ -1741,6 +1795,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
   if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
     VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
   fi
+  if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then
+    VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_METADATA_OUTPUT")
+  fi
   if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
     VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_HTML_REPORT_OUTPUT")
   fi
@@ -1788,6 +1845,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS_OUTP
   ViashError "Output file '$VIASH_PAR_RUN_PARAMS_OUTPUT' does not exist."
   exit 1
 fi
+if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then
+  ViashError "Output file '$VIASH_PAR_RUN_METADATA_OUTPUT' does not exist."
+  exit 1
+fi
 if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -e "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
   ViashError "Output file '$VIASH_PAR_HTML_REPORT_OUTPUT' does not exist."
   exit 1

target/executable/parallel_map/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -248,7 +248,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -285,11 +285,11 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -309,7 +309,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -321,7 +321,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/parallel_map/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/parallel_map/parallel_map

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# parallel_map v0.14.1
+# parallel_map v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:26Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.14.1"
+  echo "parallel_map v0.14.7"
   echo ""
   echo "Map wells in batch, using STAR"
   echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "parallel_map v0.14.1"
+            echo "parallel_map v0.14.7"
             exit
             ;;
         --input_r1)
@@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.7'
   fi
 
   # print dockerfile
@@ -1502,7 +1502,9 @@ function _run() {
 
   function is_gzipped {
     printf "Checking if input '\$1' (barcode '\$barcode') is gzipped... "
-    if file "\$1" | grep -q 'gzip'; then
+    # The file might match more than one mime-type, but if the \`-k\` flag is not
+    # set, file will only output one. 
+    if file --mime-type -k "\$1" | grep -q 'gzip'; then
       echo "Done, detected compressed file."
       return
     fi

target/executable/report/create_report/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.14.1"
+version: "v0.14.7"
 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: "v0.14.1"
+  target_tag: "v0.14.7"
   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: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -239,7 +249,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -251,7 +261,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/report/create_report/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/report/create_report/create_report

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_report v0.14.1
+# create_report v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -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="2025-11-20T19:48:23Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:02:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.14.1"
+  echo "create_report v0.14.7"
   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 v0.14.1"
+            echo "create_report v0.14.7"
             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:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.7'
   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

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. 

target/executable/stats/combine_star_logs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -175,7 +175,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -204,11 +204,11 @@ build_info:
   output: "target/executable/stats/combine_star_logs"
   executable: "target/executable/stats/combine_star_logs/combine_star_logs"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -228,7 +228,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -240,7 +240,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/stats/combine_star_logs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/stats/combine_star_logs/combine_star_logs

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# combine_star_logs v0.14.1
+# combine_star_logs v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:23Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "combine_star_logs v0.14.1"
+  echo "combine_star_logs v0.14.7"
   echo ""
   echo "Arguments:"
   echo "    --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "combine_star_logs v0.14.1"
+            echo "combine_star_logs v0.14.7"
             exit
             ;;
         --barcodes)
@@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.7'
   fi
 
   # print dockerfile

target/executable/stats/generate_pool_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -188,11 +188,11 @@ build_info:
   output: "target/executable/stats/generate_pool_statistics"
   executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -212,7 +212,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -224,7 +224,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/stats/generate_pool_statistics/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/stats/generate_pool_statistics/generate_pool_statistics

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# generate_pool_statistics v0.14.1
+# generate_pool_statistics v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_pool_statistics v0.14.1"
+  echo "generate_pool_statistics v0.14.7"
   echo ""
   echo "Arguments:"
   echo "    --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_pool_statistics v0.14.1"
+            echo "generate_pool_statistics v0.14.7"
             exit
             ;;
         --nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.7'
   fi
 
   # print dockerfile

target/executable/stats/generate_well_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -230,7 +230,7 @@ engines:
   id: "docker"
   image: "python:3.13-trixie"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -260,11 +260,11 @@ build_info:
   output: "target/executable/stats/generate_well_statistics"
   executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -284,7 +284,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -296,7 +296,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/stats/generate_well_statistics/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/stats/generate_well_statistics/generate_well_statistics

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# generate_well_statistics v0.14.1
+# generate_well_statistics v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:02:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_well_statistics v0.14.1"
+  echo "generate_well_statistics v0.14.7"
   echo ""
   echo "Generate summary statistics from BAM files generated by STAR solo."
   echo ""
@@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_well_statistics v0.14.1"
+            echo "generate_well_statistics v0.14.7"
             exit
             ;;
         --input)
@@ -861,7 +861,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.7'
   fi
 
   # print dockerfile

target/executable/utils/save_params/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "save_params"
 namespace: "utils"
-version: "v0.14.1"
+version: "v0.14.7"
 argument_groups:
 - name: "Inputs"
   arguments:
@@ -128,7 +128,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -151,11 +151,11 @@ build_info:
   output: "target/executable/utils/save_params"
   executable: "target/executable/utils/save_params/save_params"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -175,7 +175,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -187,7 +187,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/utils/save_params/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/executable/utils/save_params/save_params

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# save_params v0.14.1
+# save_params v0.14.7
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "pyyaml"
 
 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-11-20T19:48:25Z"
+LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
-LABEL org.opencontainers.image.version="v0.14.1"
+LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e"
+LABEL org.opencontainers.image.version="v0.14.7"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "save_params v0.14.1"
+  echo "save_params v0.14.7"
   echo ""
   echo "Save parameters to a YAML file"
   echo ""
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "save_params v0.14.1"
+            echo "save_params v0.14.7"
             exit
             ;;
         --id)
@@ -763,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.7'
   fi
 
   # print dockerfile

target/nextflow/eset/create_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -206,11 +206,11 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -230,7 +230,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -242,7 +242,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/eset/create_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/eset/create_eset/main.nf

@@ -1,4 +1,4 @@
-// create_eset v0.14.1
+// create_eset v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_eset",
   "namespace" : "eset",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3271,7 +3271,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3309,18 +3309,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3332,7 +3332,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3774,6 +3774,16 @@ create_eset <- function(feature_annotation_path,
                                   annotation = additional_info)
 
   eset <- eset[, colSums(exprs(eset)) != 0]
+
+  if (nrow(eset) == 0) {
+    stop("Count matrix does not seem to contain any features.")
+  }
+
+  if (ncol(eset) == 0) {
+    stop("Count matrix does not seem to contain any samples.")
+  }
+
+
   saveRDS(eset, file = output_path)
 
   message(paste0("eset created succesfully for ", ncol(eset),
@@ -4207,7 +4217,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_eset/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_eset'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
 

target/nextflow/eset/create_fdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -154,7 +154,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -183,11 +183,11 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -207,7 +207,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -219,7 +219,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/eset/create_fdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/eset/create_fdata/main.nf

@@ -1,4 +1,4 @@
-// create_fdata v0.14.1
+// create_fdata v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_fdata",
   "namespace" : "eset",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3279,18 +3279,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3302,7 +3302,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_fdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_fdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'Create a fdata file\n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/eset/create_pdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -168,7 +168,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -197,11 +197,11 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -221,7 +221,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -233,7 +233,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/eset/create_pdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/eset/create_pdata/main.nf

@@ -1,4 +1,4 @@
-// create_pdata v0.14.1
+// create_pdata v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_pdata",
   "namespace" : "eset",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3252,7 +3252,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3293,18 +3293,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3316,7 +3316,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3812,7 +3812,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_pdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_pdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'Create a pdata file by combining the mapping statistics \n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -134,7 +134,7 @@ engines:
   id: "docker"
   image: "bioconductor/bioconductor_docker:3.19"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -155,11 +155,11 @@ build_info:
   output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
   executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -179,7 +179,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -191,7 +191,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf

@@ -1,4 +1,4 @@
-// check_eset v0.14.1
+// check_eset v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "check_eset",
   "namespace" : "integration_test_components/htrnaseq",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3206,7 +3206,7 @@ meta = [
       "id" : "docker",
       "image" : "bioconductor/bioconductor_docker:3.19",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3233,18 +3233,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3256,7 +3256,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3906,7 +3906,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'integration_test_components/htrnaseq/check_eset'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'This component test the ExpressionSet object as output by the main pipeline.'
   author = 'Dries Schaumont'
 }

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,11 +164,11 @@ build_info:
   output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -188,7 +188,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -200,7 +200,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf

@@ -1,4 +1,4 @@
-// check_cutadapt_output v0.14.1
+// check_cutadapt_output v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "check_cutadapt_output",
   "namespace" : "integration_test_components/well_demultiplexing",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3213,7 +3213,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3244,18 +3244,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3267,7 +3267,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3786,7 +3786,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
   author = 'Dries Schaumont'
 }

target/nextflow/io/publish_fastqs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.14.1"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -139,11 +139,11 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -163,7 +163,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -175,7 +175,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/io/publish_fastqs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/io/publish_fastqs/main.nf

@@ -1,4 +1,4 @@
-// publish_fastqs v0.14.1
+// publish_fastqs v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish_fastqs",
   "namespace" : "io",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3184,7 +3184,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3207,18 +3207,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3230,7 +3230,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3682,7 +3682,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish_fastqs/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish_fastqs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'Publish the fastq files per well'
 }
 

target/nextflow/io/publish_results/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.14.1"
+version: "v0.14.7"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -77,6 +77,15 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output directory"
   description: "Determines the name of output directories\n"
   arguments:
@@ -158,6 +167,15 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--run_metadata_output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
   - type: "file"
     name: "--html_report_output"
     info: null
@@ -261,7 +279,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -279,11 +297,11 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -303,7 +321,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -315,7 +333,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/io/publish_results/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/io/publish_results/main.nf

@@ -1,4 +1,4 @@
-// publish_results v0.14.1
+// publish_results v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish_results",
   "namespace" : "io",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3117,6 +3117,16 @@ meta = [
           "direction" : "input",
           "multiple" : false,
           "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--run_metadata",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
         }
       ]
     },
@@ -3218,6 +3228,16 @@ meta = [
           "multiple" : false,
           "multiple_sep" : ";"
         },
+        {
+          "type" : "file",
+          "name" : "--run_metadata_output",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
         {
           "type" : "file",
           "name" : "--html_report_output",
@@ -3346,7 +3366,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3369,18 +3389,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3392,7 +3412,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3433,6 +3453,7 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#'
 $( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA+x} ]; then echo "${VIASH_PAR_RUN_METADATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_metadata='&'#" ; else echo "# par_run_metadata="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi )
@@ -3440,6 +3461,7 @@ $( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed
 $( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi )
 $( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi )
+$( if [ ! -z ${VIASH_PAR_RUN_METADATA_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_METADATA_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_metadata_output='&'#" ; else echo "# par_run_metadata_output="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
@@ -3482,6 +3504,7 @@ declare -A path_pars_dirs=(
 declare -A path_pars_files=(
   ["par_html_report_output"]="par_html_report"
   ["par_run_params_output"]="par_run_params"
+  ["par_run_metadata_output"]="par_run_metadata"
 )
 
 echo "Canonicalizing output paths."
@@ -3909,7 +3932,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish_results/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish_results'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.14.1'
+  version = 'v0.14.7'
   description = 'Publish the results'
 }
 

target/nextflow/io/publish_results/nextflow_schema.json

@@ -82,6 +82,13 @@
           "exists": true,
           "description": "",
           "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
+        },
+        "run_metadata": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
         }
       }
     },
@@ -146,6 +153,13 @@
           "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_params_output\"`, direction: `output`. ",
           "default": "$id.$key.run_params_output"
         },
+        "run_metadata_output": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_metadata_output\"`, direction: `output`. ",
+          "default": "$id.$key.run_metadata_output"
+        },
         "html_report_output": {
           "type": "string",
           "format": "path",

target/nextflow/parallel_map/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.14.1"
+version: "v0.14.7"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -248,7 +248,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.14.1"
+  target_tag: "v0.14.7"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -285,11 +285,11 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.4"
-  git_commit: "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13"
+  git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
-  version: "v0.14.1"
+  version: "v0.14.7"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -309,7 +309,7 @@ package_config:
     \ first.\n"
   info:
     test_resources:
-    - path: "gs://viash-hub-resources/htrnaseq/v2"
+    - path: "gs://viash-hub-resources/htrnaseq/v4"
       dest: "resources_test"
   viash_version: "0.9.4"
   source: "src"
@@ -321,7 +321,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/parallel_map/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.14.1
+version: v0.14.7
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
@@ -11,7 +11,7 @@ links:
 viash_version: 0.9.4
 info:
   test_resources:
-    - path: gs://viash-hub-resources/htrnaseq/v2
+    - path: gs://viash-hub-resources/htrnaseq/v4
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']

target/nextflow/parallel_map/main.nf

@@ -1,4 +1,4 @@
-// parallel_map v0.14.1
+// parallel_map v0.14.7
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "parallel_map",
-  "version" : "v0.14.1",
+  "version" : "v0.14.7",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3332,7 +3332,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.14.1",
+      "target_tag" : "v0.14.7",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3379,18 +3379,18 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.4",
-    "git_commit" : "2b3dbd8515c074b32732d3848b0d2db6fcc8cc13",
+    "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.14.1",
+    "version" : "v0.14.7",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
       "test_resources" : [
         {
-          "path" : "gs://viash-hub-resources/htrnaseq/v2",
+          "path" : "gs://viash-hub-resources/htrnaseq/v4",
           "dest" : "resources_test"
         }
       ]
@@ -3402,7 +3402,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.14.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.14.7'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3624,7 +3624,9 @@ function _run() {
 
   function is_gzipped {
     printf "Checking if input '\\$1' (barcode '\\$barcode') is gzipped... "
-    if file "\\$1" | grep -q 'gzip'; then
+    # The file might match more than one mime-type, but if the \\`-k\\` flag is not
+    # set, file will only output one. 
+    if file --mime-type -k "\\$1" | grep -q 'gzip'; then
       echo "Done, detected compressed file."
       return
     fi
@@ -4171,7 +4173,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.14.1"
+    "tag" : "v0.14.7"
   },
   "tag" : "$id"
 }'''),