diff --git a/.gitignore b/.gitignore
index 7f20e6ac..53fcf2b6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 target
 testData
+resources_test
 
 # Nextflow related files
 .nextflow
diff --git a/_viash.yaml b/_viash.yaml
index 38f36696..54d96fa9 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -50,7 +50,7 @@ info:
 
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 
diff --git a/src/io/publish_results/code.sh b/src/io/publish_results/code.sh
index 72dd5ed5..62349343 100755
--- a/src/io/publish_results/code.sh
+++ b/src/io/publish_results/code.sh
@@ -1,44 +1,93 @@
 #!/bin/bash
 
-echo "Publishing $par_input -> $par_output"
+set -eo pipefail
+
+echo "Publishing results to multiple output directories"
+
+# Create output directories for multiple files
+echo "Creating output directories..."
+
+path_pars=(
+  par_star_output_dir
+  par_nrReadsNrGenesPerChrom_dir
+  par_star_qc_metrics_dir
+  par_eset_dir
+  par_f_data_dir
+  par_p_data_dir
+  par_html_report_output
+  par_run_params_output
+)
+
+for par in ${path_pars[@]}; do
+    curr_val="${!par}"
+    new_value=$(realpath --canonicalize-missing "$curr_val")
+    declare -g "$par=$new_value"
+done
+
+mkdir -p "$par_star_output_dir" && echo "$par_star_output_dir created"
+mkdir -p "$par_nrReadsNrGenesPerChrom_dir" && echo "$par_nrReadsNrGenesPerChrom_dir created"  
+mkdir -p "$par_star_qc_metrics_dir" && echo "$par_star_qc_metrics_dir created"
+mkdir -p "$par_eset_dir" && echo "$par_eset_dir created"
+mkdir -p "$par_f_data_dir" && echo "$par_f_data_dir created"
+mkdir -p "$par_p_data_dir" && echo "$par_p_data_dir created"
 
 echo
-echo "Creating directory if it does not exist:"
-mkdir -p "$par_output" && echo "$par_output created"
-
-echo
-echo "Copying files..."
+echo "Copying STAR output files..."
 IFS=";" read -ra star_output <<<$par_star_output
-IFS=";" read -ra nrReadsNrGenesPerChrom <<<$par_nrReadsNrGenesPerChrom
-IFS=";" read -ra star_qc_metrics <<<$par_star_qc_metrics
-IFS=";" read -ra eset <<<$par_eset
-IFS=";" read -ra f_data <<<$par_f_data
-IFS=";" read -ra p_data <<<$par_p_data
-
 for i in "${star_output[@]}"; do
-  cp -rL "$i" "$par_output/"
+  echo "Copying $i to $par_star_output_dir/"
+  cp -rL "$i" "$par_star_output_dir/"
 done
 
+echo
+echo "Copying nrReadsNrGenesPerChrom files..."
+IFS=";" read -ra nrReadsNrGenesPerChrom <<<$par_nrReadsNrGenesPerChrom
 for i in "${nrReadsNrGenesPerChrom[@]}"; do
-  cp -rL "$i" "$par_output/"
+  echo "Copying $i to $par_nrReadsNrGenesPerChrom_dir/"
+  cp -rL "$i" "$par_nrReadsNrGenesPerChrom_dir/"
 done
 
+echo
+echo "Copying STAR QC metrics files..."
+IFS=";" read -ra star_qc_metrics <<<$par_star_qc_metrics
 for i in "${star_qc_metrics[@]}"; do
-  cp -rL "$i" "$par_output/"
+  echo "Copying $i to $par_star_qc_metrics_dir/"
+  cp -rL "$i" "$par_star_qc_metrics_dir/"
 done
 
+echo
+echo "Copying eset files..."
+IFS=";" read -ra eset <<<$par_eset
 for i in "${eset[@]}"; do
-  cp -rL "$i" "$par_output/"
+  echo "Copying $i to $par_eset_dir/"
+  cp -rL "$i" "$par_eset_dir/"
 done
 
+echo
+echo "Copying f_data files..."
+IFS=";" read -ra f_data <<<$par_f_data
 for i in "${f_data[@]}"; do
-  cp -rL "$i" "$par_output/"
+  echo "Copying $i to $par_f_data_dir/"
+  cp -rL "$i" "$par_f_data_dir/"
 done
 
+echo
+echo "Copying p_data files..."
+IFS=";" read -ra p_data <<<$par_p_data
 for i in "${p_data[@]}"; do
-  cp -rL "$i" "$par_output/"
+  echo "Copying $i to $par_p_data_dir/"
+  cp -rL "$i" "$par_p_data_dir/"
 done
 
-cp -rL "$par_html_report" "$par_output/"
+echo
+echo "Copying single files directly..."
+mkdir -p $(dirname "$par_html_report_output")
+echo "Copying $par_html_report to $par_html_report_output"
+cp -L "$par_html_report" "$par_html_report_output"
 
-cp -rL "$par_run_params" "$par_output/"
+echo "Copying $par_run_params to $par_run_params_output"
+mkdir -p $(dirname "$par_run_params_output")
+cp -L "$par_run_params" "$par_run_params_output"
+
+echo
+echo "Publishing completed successfully!"
diff --git a/src/io/publish_results/config.vsh.yaml b/src/io/publish_results/config.vsh.yaml
index 5c294aba..6da4c312 100644
--- a/src/io/publish_results/config.vsh.yaml
+++ b/src/io/publish_results/config.vsh.yaml
@@ -35,13 +35,44 @@ argument_groups:
       - name: "--run_params"
         type: file
         required: true
-  - name: Output arguments
+  - name: Output directory
+    description: |
+      Determines the name of output directories
     arguments:
-      - name: --output
+      - name: --star_output_dir
         type: file
         direction: output
-        # ID is the well barcode
-        default: "$id/"
+        default: "star_output"
+      - name: --nrReadsNrGenesPerChrom_dir
+        type: file
+        direction: output
+        default: "nrReadsNrGenesPerChrom"
+      - name: --star_qc_metrics_dir
+        type: file
+        direction: output
+        default: "starLogs"
+      - name: --eset_dir
+        type: file
+        direction: output
+        default: "esets"
+      - name: --f_data_dir
+        type: file
+        direction: output
+        default: "fData"
+      - name: --p_data_dir
+        type: file
+        direction: output
+        default: "pData"
+  - name: "Output file arguments"
+    description: Determines the name of output files
+    arguments:
+      - name: "--run_params_output"
+        type: file
+        direction: output
+      - name: "--html_report_output"
+        type: file
+        direction: output
+
 
 resources:
   - type: bash_script
diff --git a/src/workflows/htrnaseq/main.nf b/src/workflows/htrnaseq/main.nf
index 9b32050b..6b7fb1a4 100644
--- a/src/workflows/htrnaseq/main.nf
+++ b/src/workflows/htrnaseq/main.nf
@@ -344,7 +344,6 @@ workflow run_wf {
       | setState([
         "star_output": "star_output",
         "fastq_output": "fastq_output_directory",
-        "star_output": "star_output",
         "nrReadsNrGenesPerChrom": "nrReadsNrGenesPerChromPool",
         "star_qc_metrics": "star_qc_metrics",
         "eset": "eset",
diff --git a/src/workflows/runner/config.vsh.yaml b/src/workflows/runner/config.vsh.yaml
index 26509a23..b6101e8a 100644
--- a/src/workflows/runner/config.vsh.yaml
+++ b/src/workflows/runner/config.vsh.yaml
@@ -66,15 +66,36 @@ argument_groups:
         required: true
   - name: Output arguments
     arguments:
-    - name: "--eset_output"
-      type: file
-      direction: output
-      default: esets
+      - name: "--star_output_dir"
+        type: file
+        direction: output
+        default: "star_output"
+      - name: "--nrReadsNrGenesPerChrom_dir"
+        type: file
+        direction: output
+        default: "nrReadsNrGenesPerChrom"
+      - name: "--star_qc_metrics_dir"
+        type: file
+        direction: output
+        default: "starLogs"
+      - name: "--eset_dir"
+        type: file
+        direction: output
+        default: "esets"
+      - name: "--f_data_dir"
+        type: file
+        direction: output
+        default: "fData"
+      - name: "--p_data_dir"
+        type: file
+        direction: output
+        default: "pData"
 
 resources:
   - type: nextflow_script
     path: main.nf
     entrypoint: run_wf
+  - path: disable_publishfiles_process.config
 
 test_resources:
   - type: nextflow_script
@@ -95,6 +116,9 @@ dependencies:
 
 runners:
   - type: nextflow
+    config: 
+      script: 
+        - includeConfig("disable_publishfiles_process.config")
 
 engines:
   - type: native
diff --git a/src/workflows/runner/disable_publishfiles_process.config b/src/workflows/runner/disable_publishfiles_process.config
new file mode 100644
index 00000000..6cff5e26
--- /dev/null
+++ b/src/workflows/runner/disable_publishfiles_process.config
@@ -0,0 +1,5 @@
+process {
+  withName: publishFilesProc {
+    publishDir = [ enabled: false ]
+  }
+}
\ No newline at end of file
diff --git a/src/workflows/runner/integration_test.sh b/src/workflows/runner/integration_test.sh
index 57531155..eb67d014 100755
--- a/src/workflows/runner/integration_test.sh
+++ b/src/workflows/runner/integration_test.sh
@@ -1,6 +1,8 @@
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
+set -eo pipefail
+
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf
index 515cf565..d2111352 100644
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -26,7 +26,6 @@ workflow run_wf {
         def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states]
         return [new_id, new_state]
       }
-
       | save_params.run(
         key: "save_params_runner",
         fromState: {id, state ->
@@ -60,6 +59,19 @@ workflow run_wf {
       )
     
     htrnaseq_ch = input_ch
+      | map { id, state -> 
+        // The argument names for this workflow and the htrnaseq workflow may overlap
+        // here, we store a copy in order to make sure to not accidentally overwrite the state.
+        def new_state = state + [
+          "star_output_dir_workflow": state.star_output_dir,
+          "nrReadsNrGenesPerChrom_dir_workflow": state.nrReadsNrGenesPerChrom_dir,
+          "star_qc_metrics_dir_workflow": state.star_qc_metrics_dir,
+          "eset_dir_workflow": state.eset_dir,
+          "f_data_dir_workflow": state.f_data_dir,
+          "p_data_dir_workflow": state.p_data_dir
+        ]
+        return [id, new_state]
+      }
       | listInputDir.run(
         fromState: [
           "input": "input",
@@ -119,49 +131,81 @@ workflow run_wf {
         toState: { id, result, state -> state + result }
       )
 
-      // The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
-      // but for publishing the results, this is not handy because we want to use the $id
-      // variable as a pointer to the target data.
-      //
-      // So, we should combine everything together
-      //
-      // project_id / experiment_id / "data_processed" / date_workflow
-    grouped_ch = htrnaseq_ch
-      | toSortedList
-      | map{ vs ->
-          def all_fastqs
-          [
-            vs[0][1].run_id, // The original ID
-            [
-              star_output: reduce_paths(vs.collect{ it[1].star_output }.flatten()),
-              nrReadsNrGenesPerChrom: reduce_paths(vs.collect{ it[1].nrReadsNrGenesPerChrom }),
-              star_qc_metrics: reduce_paths(vs.collect{ it[1].star_qc_metrics }),
-              eset: reduce_paths(vs.collect{ it[1].eset }),
-              f_data: reduce_paths(vs.collect{ it[1].f_data }),
-              p_data: reduce_paths(vs.collect{ it[1].p_data }),
-              fastq_output: vs.collect{ it[1].fastq_output }.flatten().unique(),
-              html_report: vs.collect{ it[1].html_report }[0],  // The report is for all pools
-              plain_output: vs.collect{ it[1].plain_output }[0],
-              project_id: vs.collect{ it[1].project_id }[0],
-              experiment_id: vs.collect{ it[1].experiment_id }[0]
-            ]
-          ]
-        }
-
-    grouped_with_params_list_ch = grouped_ch.combine(save_params_ch)
+    // The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
+    // but for publishing the results, this is not handy because we want to use the $id
+    // variable as a pointer to the target data.
+    // So, we should combine everything together
+    results_publish_ch = htrnaseq_ch
+      | combine(save_params_ch)
       | map {new_id, grouped_ch_state, save_params_id, save_params_state ->
         def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
         return [new_id, new_state]
-      
       }
+      | toSortedList
+      | map{ vs ->
+          def states = vs.collect{it[1]}
 
-    results_publish_ch = grouped_with_params_list_ch
+          // The STAR output is a directory for each well in a plate (or pool of plates).
+          // The wells are grouped into a directory per sample. The name of this directory should
+          // match the sample_id.
+          def star_output_samples = states.collectMany{state -> 
+            state.star_output.collect{
+              def star_sample_dir = it.parent
+              assert star_sample_dir.name == state.sample_id: "Unexpected state: the parent directory of STAR output \
+                path '${it}' should match with the sample ID ${sample_id}"
+              star_sample_dir
+            }
+          }
+          def new_state = [
+            "star_output": star_output_samples,
+          ]
+
+          // Keys for which the values should be the same across samples
+          def state_keys_unique = [
+            "html_report",
+            "project_id",
+            "experiment_id",
+            "star_output_dir_workflow",
+            "nrReadsNrGenesPerChrom_dir_workflow",
+            "star_qc_metrics_dir_workflow",
+            "eset_dir_workflow",
+            "f_data_dir_workflow",
+            "p_data_dir_workflow",
+            "f_data",
+            "run_params"
+          ]
+          def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name ->
+            argument_values = states.collect{it.get(argument_name)}.unique()
+            assert argument_values.size() == 1, "State error: values for argument $argument_name should be the same across states. \
+                                                 Argument values: $argument_values"
+            // take the unique value from the set (there is only one)
+            def argument_value
+            argument_values.each { argument_value = it }
+            state_to_update + [(argument_name): argument_value]
+          }
+
+          // Keys that just require gathering of values across samples
+          def state_keys_collect = [
+            "nrReadsNrGenesPerChrom",
+            "star_qc_metrics",
+            "eset",
+            "p_data",
+          ]
+          def state_collect = state_keys_collect.collectEntries{ key_ ->
+            [key_, states.collect{it.get(key_)}]
+          }
+
+          new_state = new_state + state_unique_keys + state_collect
+          [states[0].run_id, new_state]  
+      }
       | publish_results.run(
         fromState: { id, state ->
-          def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
-          println("Publising results to ${params.results_publish_dir}/${output_dir}")
+          def prefix = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
 
-          [
+          println("Publising results to ${params.results_publish_dir}/${prefix}")
+
+          [ 
+            // Inputs
             star_output: state.star_output,
             nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom,
             star_qc_metrics: state.star_qc_metrics,
@@ -170,10 +214,18 @@ workflow run_wf {
             p_data: state.p_data,
             html_report: state.html_report,
             run_params: state.run_params,
-            output: output_dir.toString()
+            // Output locations
+            run_params_output: "${prefix}/${state.run_params.name}",
+            html_report_output: "${prefix}/${state.html_report.name}", 
+            star_output_dir: "${prefix}/${state.star_output_dir_workflow}",
+            nrReadsNrGenesPerChrom_dir: "${prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}",
+            star_qc_metrics_dir: "${prefix}/${state.star_qc_metrics_dir_workflow}",
+            eset_dir: "${prefix}/${state.eset_dir_workflow}",
+            f_data_dir: "${prefix}/${state.f_data_dir_workflow}",
+            p_data_dir: "${prefix}/${state.p_data_dir_workflow}"
           ]
         },
-        toState: { id, result, state -> state + ["eset_output": state.eset] },
+        toState: { id, result, state -> result },
         directives: [
           publishDir: [
             path: "${params.results_publish_dir}", 
@@ -182,33 +234,43 @@ workflow run_wf {
           ]
         ]
       )
+      | setState([
+          "star_output_dir",
+          "nrReadsNrGenesPerChrom_dir",
+          "star_qc_metrics_dir",
+          "eset_dir",
+          "f_data_dir",
+          "p_data_dir",
+        ]
+      )
 
-    fastq_publish_ch = grouped_ch
-      | flatMap{id, state ->
-        def new_states = state.fastq_output.collect{fastq_dir -> 
-          def run_id = fastq_dir.name // The folder name corresponds to the run
-          def sample = fastq_dir.parent.name // The parent folder name should be the sample
-          def new_id = "${run_id}/${sample}"
-          def fastq_files = fastq_dir.listFiles()
-          def new_state = [
-            "fastq_output": fastq_files,
-            "sample_id": sample,
-            "run_id": run_id 
-          ]
-          return [new_id, new_state]
-        }
-        return new_states
+    fastq_publish_ch = htrnaseq_ch
+      // The output from the htrnaseq workflow is on sample (i.e. pool) level
+      // Multiple sequencing runs may have contributes to the FASTQ files from this pool.
+      // So the fastq_output is a list of directories, one for each run.
+      // We assume that the names of the folders containing the FASTQ files are equal to the pool names.
+      | flatMap {id, state ->
+          state.fastq_output.collect{fastq_dir ->
+            def run_id = fastq_dir.name
+            def new_id = "${run_id}/${state.sample_id}"
+            def new_state = [
+              "fastq_output": fastq_dir.listFiles(),
+              "sample_id": state.sample_id,
+              "run_id": run_id,
+              "output": "${run_id}/${date}_htrnaseq_${version}/${state.sample_id}".toString()
+            ]
+            [new_id, new_state]
+          }
       }
+      // A folder containing the FASTQ files from a certain pool may be present in the state from
+      // multiple samples; if that pool contributed to the data from those samples.
+      // Those FASTQ files will only be published once by filtering out the duplicate events here.
+      | unique{it[0]}
       | publish_fastqs.run(
-        fromState: { id, state ->
-          def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
-          println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}")
-
-          [
-            input: state.fastq_output,
-            output: output_dir.toString(),
-          ]
-        },
+        fromState: [
+          "input": "fastq_output",
+          "output": "output",
+        ],
         toState: { id, result, state -> state },
         directives: [
           publishDir: [
@@ -219,12 +281,9 @@ workflow run_wf {
         ]
       )
 
-    output_ch = results_publish_ch
-      | setState(["eset_output"])
-
   emit:
-    grouped_ch
-      | map{ id, state -> [ id, [ _meta: [ join_id: state.run_id ] ] ] }
+    results_publish_ch
+
 }
 
 def get_version(inputFile) {
@@ -233,37 +292,4 @@ def get_version(inputFile) {
   def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
   println("HT-RNAseq version to be used: ${version}")
   return version
-}
-
-/*
- * This function uses a heuristic to group a list of paths so that the level of nesting
- * of IDs is represented in the output.
- *
- * We iterative of the path sections (subfolders) from the last (file) the first (root node).
- * The first path segment that is common across all 'events' is the cutoff. We cutoff the paths
- * at this level, select the unique elements from the list and use that as input for the next step.
- *
- * An optional offset allows one to shift the cutoff left or right.
- */
-def reduce_paths(paths, offset = 0) {
-  def path_length = paths.collect{ it.getNameCount() }[0]
-
-  def unique_list = (path_length-1..0).collectEntries { i ->
-    [ (i): paths.collect{ it.getName(i) }.unique().size() ]
-  }
-
-  def cutoff = unique_list.find{ it.value == 1 }.key
-
-  def grouped_paths = paths.collect{ f -> "/" + f.subpath(0, cutoff+1+offset) }.unique()
-
-  println("")
-  println("Detecting the common path section to pass to the next step:")
-  print("  From: ")
-  print paths
-  println("")
-  print("  To:   ")
-  print grouped_paths
-  println("")
-
-  return grouped_paths
 }
\ No newline at end of file
diff --git a/src/workflows/runner/test.nf b/src/workflows/runner/test.nf
index ea020c11..c9269907 100644
--- a/src/workflows/runner/test.nf
+++ b/src/workflows/runner/test.nf
@@ -36,7 +36,8 @@ if (!params.containsKey("publish_dir")) {
 
 params.fastq_publish_dir = (file(params.publish_dir) / "fastq").toUriString()
 params.results_publish_dir = (file(params.publish_dir) / "results").toUriString()
-
+assert file(params.fastq_publish_dir).isEmpty()
+assert file(params.results_publish_dir).isEmpty()
 
 // The module inherits the parameters defined before the include statement, 
 // therefore any parameters set afterwards will not be used by the module.
@@ -99,6 +100,17 @@ workflow test_wf {
     | toSortedList()
     | map {events ->
         assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
+        events
+    }
+    | map {states -> 
+        def output_state = states[0][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).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()
     }
 
 
@@ -172,7 +184,7 @@ workflow test_wf {
             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.gencode.v41.annotation.gtf.gz.txt").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)
@@ -309,7 +321,7 @@ workflow test_wf_with_lanes {
             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.gencode.v41.annotation.gtf.gz.txt").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)
diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml
index 7d288625..0550c682 100644
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -206,9 +206,9 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -238,7 +238,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/eset/create_eset/_viash.yaml b/target/executable/eset/create_eset/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/eset/create_eset/_viash.yaml
+++ b/target/executable/eset/create_eset/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset
index 5369e231..3057d1b0 100755
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -456,9 +456,9 @@ 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="2025-08-22T08:16:48Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml
index 04ec3f20..132c2d7a 100644
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -215,7 +215,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/eset/create_fdata/_viash.yaml b/target/executable/eset/create_fdata/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/eset/create_fdata/_viash.yaml
+++ b/target/executable/eset/create_fdata/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata
index 1c95466a..4484b331 100755
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -458,9 +458,9 @@ 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="2025-08-22T08:16:49Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml
index 1c52688f..9c07a78a 100644
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -197,9 +197,9 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -229,7 +229,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/eset/create_pdata/_viash.yaml b/target/executable/eset/create_pdata/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/eset/create_pdata/_viash.yaml
+++ b/target/executable/eset/create_pdata/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata
index 3dd9ad35..abc94620 100755
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -458,9 +458,9 @@ 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="2025-08-22T08:16:48Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 922154d6..ac605de5 100644
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -155,9 +155,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -187,7 +187,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
index f70a9741..0c9aa98a 100755
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -455,9 +455,9 @@ 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="2025-08-22T08:16:49Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index a40e60ff..9d93fb33 100644
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -164,9 +164,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -196,7 +196,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
index d73d7bf5..5ecf0e27 100755
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -457,9 +457,9 @@ 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="2025-08-22T08:16:49Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml
index ab0341e9..fbada63f 100644
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -139,9 +139,9 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -171,7 +171,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/io/publish_fastqs/_viash.yaml b/target/executable/io/publish_fastqs/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/io/publish_fastqs/_viash.yaml
+++ b/target/executable/io/publish_fastqs/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs
index 99c6307b..8a8b8616 100755
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -450,9 +450,9 @@ 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="2025-08-22T08:16:50Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml
index c658d4ea..96071baf 100644
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -77,13 +77,90 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
-- name: "Output arguments"
+- name: "Output directory"
+  description: "Determines the name of output directories\n"
   arguments:
   - type: "file"
-    name: "--output"
+    name: "--star_output_dir"
     info: null
     default:
-    - "$id"
+    - "star_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--nrReadsNrGenesPerChrom_dir"
+    info: null
+    default:
+    - "nrReadsNrGenesPerChrom"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_qc_metrics_dir"
+    info: null
+    default:
+    - "starLogs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--eset_dir"
+    info: null
+    default:
+    - "esets"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--f_data_dir"
+    info: null
+    default:
+    - "fData"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--p_data_dir"
+    info: null
+    default:
+    - "pData"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output file arguments"
+  description: "Determines the name of output files"
+  arguments:
+  - type: "file"
+    name: "--run_params_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
     must_exist: true
     create_parent: true
     required: false
@@ -202,9 +279,9 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -234,7 +311,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/io/publish_results/_viash.yaml b/target/executable/io/publish_results/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/io/publish_results/_viash.yaml
+++ b/target/executable/io/publish_results/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results
index 0afa282a..2a92bda6 100755
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -450,9 +450,9 @@ 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="2025-08-22T08:16:50Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
@@ -600,10 +600,41 @@ function ViashHelp {
   echo "    --run_params"
   echo "        type: file, required parameter, file must exist"
   echo ""
-  echo "Output arguments:"
-  echo "    --output"
+  echo "Output directory:"
+  echo "    Determines the name of output directories"
+  echo ""
+  echo "    --star_output_dir"
+  echo "        type: file, output, file must exist"
+  echo "        default: star_output"
+  echo ""
+  echo "    --nrReadsNrGenesPerChrom_dir"
+  echo "        type: file, output, file must exist"
+  echo "        default: nrReadsNrGenesPerChrom"
+  echo ""
+  echo "    --star_qc_metrics_dir"
+  echo "        type: file, output, file must exist"
+  echo "        default: starLogs"
+  echo ""
+  echo "    --eset_dir"
+  echo "        type: file, output, file must exist"
+  echo "        default: esets"
+  echo ""
+  echo "    --f_data_dir"
+  echo "        type: file, output, file must exist"
+  echo "        default: fData"
+  echo ""
+  echo "    --p_data_dir"
+  echo "        type: file, output, file must exist"
+  echo "        default: pData"
+  echo ""
+  echo "Output file arguments:"
+  echo "    Determines the name of output files"
+  echo ""
+  echo "    --run_params_output"
+  echo "        type: file, output, file must exist"
+  echo ""
+  echo "    --html_report_output"
   echo "        type: file, output, file must exist"
-  echo "        default: \$id"
   echo ""
   echo "Viash built in Computational Requirements:"
   echo "    ---cpus=INT"
@@ -779,15 +810,92 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_RUN_PARAMS=$(ViashRemoveFlags "$1")
             shift 1
             ;;
-        --output)
-            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_OUTPUT="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
+        --star_output_dir)
+            [ -n "$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"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --star_output_dir. Use "--help" to get more information on the parameters. && exit 1
             shift 2
             ;;
-        --output=*)
-            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
+        --star_output_dir=*)
+            [ -n "$VIASH_PAR_STAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--star_output_dir=*\': \'$VIASH_PAR_STAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STAR_OUTPUT_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --nrReadsNrGenesPerChrom_dir)
+            [ -n "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && ViashError Bad arguments for option \'--nrReadsNrGenesPerChrom_dir\': \'$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NRREADSNRGENESPERCHROM_DIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --nrReadsNrGenesPerChrom_dir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --nrReadsNrGenesPerChrom_dir=*)
+            [ -n "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && ViashError Bad arguments for option \'--nrReadsNrGenesPerChrom_dir=*\': \'$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NRREADSNRGENESPERCHROM_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --star_qc_metrics_dir)
+            [ -n "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && ViashError Bad arguments for option \'--star_qc_metrics_dir\': \'$VIASH_PAR_STAR_QC_METRICS_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STAR_QC_METRICS_DIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --star_qc_metrics_dir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --star_qc_metrics_dir=*)
+            [ -n "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && ViashError Bad arguments for option \'--star_qc_metrics_dir=*\': \'$VIASH_PAR_STAR_QC_METRICS_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STAR_QC_METRICS_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --eset_dir)
+            [ -n "$VIASH_PAR_ESET_DIR" ] && ViashError Bad arguments for option \'--eset_dir\': \'$VIASH_PAR_ESET_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ESET_DIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --eset_dir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --eset_dir=*)
+            [ -n "$VIASH_PAR_ESET_DIR" ] && ViashError Bad arguments for option \'--eset_dir=*\': \'$VIASH_PAR_ESET_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ESET_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --f_data_dir)
+            [ -n "$VIASH_PAR_F_DATA_DIR" ] && ViashError Bad arguments for option \'--f_data_dir\': \'$VIASH_PAR_F_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_F_DATA_DIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --f_data_dir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --f_data_dir=*)
+            [ -n "$VIASH_PAR_F_DATA_DIR" ] && ViashError Bad arguments for option \'--f_data_dir=*\': \'$VIASH_PAR_F_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_F_DATA_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --p_data_dir)
+            [ -n "$VIASH_PAR_P_DATA_DIR" ] && ViashError Bad arguments for option \'--p_data_dir\': \'$VIASH_PAR_P_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_P_DATA_DIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --p_data_dir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --p_data_dir=*)
+            [ -n "$VIASH_PAR_P_DATA_DIR" ] && ViashError Bad arguments for option \'--p_data_dir=*\': \'$VIASH_PAR_P_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_P_DATA_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --run_params_output)
+            [ -n "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && ViashError Bad arguments for option \'--run_params_output\': \'$VIASH_PAR_RUN_PARAMS_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_PARAMS_OUTPUT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_params_output. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --run_params_output=*)
+            [ -n "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && ViashError Bad arguments for option \'--run_params_output=*\': \'$VIASH_PAR_RUN_PARAMS_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_RUN_PARAMS_OUTPUT=$(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"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --html_report_output. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --html_report_output=*)
+            [ -n "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && ViashError Bad arguments for option \'--html_report_output=*\': \'$VIASH_PAR_HTML_REPORT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashRemoveFlags "$1")
             shift 1
             ;;
         ---engine)
@@ -1020,8 +1128,23 @@ if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
 fi
 
 # filling in defaults
-if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
-  VIASH_PAR_OUTPUT="\$id"
+if [ -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then
+  VIASH_PAR_STAR_OUTPUT_DIR="star_output"
+fi
+if [ -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then
+  VIASH_PAR_NRREADSNRGENESPERCHROM_DIR="nrReadsNrGenesPerChrom"
+fi
+if [ -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then
+  VIASH_PAR_STAR_QC_METRICS_DIR="starLogs"
+fi
+if [ -z ${VIASH_PAR_ESET_DIR+x} ]; then
+  VIASH_PAR_ESET_DIR="esets"
+fi
+if [ -z ${VIASH_PAR_F_DATA_DIR+x} ]; then
+  VIASH_PAR_F_DATA_DIR="fData"
+fi
+if [ -z ${VIASH_PAR_P_DATA_DIR+x} ]; then
+  VIASH_PAR_P_DATA_DIR="pData"
 fi
 
 # check whether required files exist
@@ -1181,8 +1304,29 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
 fi
 
 # create parent directories of output files, if so desired
-if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
-  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
+if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_STAR_OUTPUT_DIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_STAR_OUTPUT_DIR")"
+fi
+if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")"
+fi
+if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_STAR_QC_METRICS_DIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_STAR_QC_METRICS_DIR")"
+fi
+if [ ! -z "$VIASH_PAR_ESET_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_ESET_DIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_ESET_DIR")"
+fi
+if [ ! -z "$VIASH_PAR_F_DATA_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_F_DATA_DIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_F_DATA_DIR")"
+fi
+if [ ! -z "$VIASH_PAR_P_DATA_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_P_DATA_DIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_P_DATA_DIR")"
+fi
+if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")"
+fi
+if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")"
 fi
 
 if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
@@ -1271,10 +1415,45 @@ if [ ! -z "$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 "$VIASH_PAR_OUTPUT" ]; then
-  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
-  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
-  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
+if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_OUTPUT_DIR")" )
+  VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_OUTPUT_DIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_STAR_OUTPUT_DIR" )
+fi
+if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")" )
+  VIASH_PAR_NRREADSNRGENESPERCHROM_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" )
+fi
+if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_QC_METRICS_DIR")" )
+  VIASH_PAR_STAR_QC_METRICS_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_QC_METRICS_DIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_STAR_QC_METRICS_DIR" )
+fi
+if [ ! -z "$VIASH_PAR_ESET_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ESET_DIR")" )
+  VIASH_PAR_ESET_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_ESET_DIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_ESET_DIR" )
+fi
+if [ ! -z "$VIASH_PAR_F_DATA_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_F_DATA_DIR")" )
+  VIASH_PAR_F_DATA_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_F_DATA_DIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_F_DATA_DIR" )
+fi
+if [ ! -z "$VIASH_PAR_P_DATA_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_P_DATA_DIR")" )
+  VIASH_PAR_P_DATA_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_P_DATA_DIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_P_DATA_DIR" )
+fi
+if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_PARAMS_OUTPUT")" )
+  VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_PARAMS_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 "$VIASH_PAR_HTML_REPORT_OUTPUT")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_HTML_REPORT_OUTPUT" )
 fi
 if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
@@ -1353,7 +1532,14 @@ $( 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 ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; 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 )
+$( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_eset_dir='&'#" ; else echo "# par_eset_dir="; fi )
+$( 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 ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${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 )
 $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1376,48 +1562,97 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 ## VIASH END
 #!/bin/bash
 
-echo "Publishing \$par_input -> \$par_output"
+set -eo pipefail
+
+echo "Publishing results to multiple output directories"
+
+# Create output directories for multiple files
+echo "Creating output directories..."
+
+path_pars=(
+  par_star_output_dir
+  par_nrReadsNrGenesPerChrom_dir
+  par_star_qc_metrics_dir
+  par_eset_dir
+  par_f_data_dir
+  par_p_data_dir
+  par_html_report_output
+  par_run_params_output
+)
+
+for par in \${path_pars[@]}; do
+    curr_val="\${!par}"
+    new_value=\$(realpath --canonicalize-missing "\$curr_val")
+    declare -g "\$par=\$new_value"
+done
+
+mkdir -p "\$par_star_output_dir" && echo "\$par_star_output_dir created"
+mkdir -p "\$par_nrReadsNrGenesPerChrom_dir" && echo "\$par_nrReadsNrGenesPerChrom_dir created"  
+mkdir -p "\$par_star_qc_metrics_dir" && echo "\$par_star_qc_metrics_dir created"
+mkdir -p "\$par_eset_dir" && echo "\$par_eset_dir created"
+mkdir -p "\$par_f_data_dir" && echo "\$par_f_data_dir created"
+mkdir -p "\$par_p_data_dir" && echo "\$par_p_data_dir created"
 
 echo
-echo "Creating directory if it does not exist:"
-mkdir -p "\$par_output" && echo "\$par_output created"
-
-echo
-echo "Copying files..."
+echo "Copying STAR output files..."
 IFS=";" read -ra star_output <<<\$par_star_output
-IFS=";" read -ra nrReadsNrGenesPerChrom <<<\$par_nrReadsNrGenesPerChrom
-IFS=";" read -ra star_qc_metrics <<<\$par_star_qc_metrics
-IFS=";" read -ra eset <<<\$par_eset
-IFS=";" read -ra f_data <<<\$par_f_data
-IFS=";" read -ra p_data <<<\$par_p_data
-
 for i in "\${star_output[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  echo "Copying \$i to \$par_star_output_dir/"
+  cp -rL "\$i" "\$par_star_output_dir/"
 done
 
+echo
+echo "Copying nrReadsNrGenesPerChrom files..."
+IFS=";" read -ra nrReadsNrGenesPerChrom <<<\$par_nrReadsNrGenesPerChrom
 for i in "\${nrReadsNrGenesPerChrom[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  echo "Copying \$i to \$par_nrReadsNrGenesPerChrom_dir/"
+  cp -rL "\$i" "\$par_nrReadsNrGenesPerChrom_dir/"
 done
 
+echo
+echo "Copying STAR QC metrics files..."
+IFS=";" read -ra star_qc_metrics <<<\$par_star_qc_metrics
 for i in "\${star_qc_metrics[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  echo "Copying \$i to \$par_star_qc_metrics_dir/"
+  cp -rL "\$i" "\$par_star_qc_metrics_dir/"
 done
 
+echo
+echo "Copying eset files..."
+IFS=";" read -ra eset <<<\$par_eset
 for i in "\${eset[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  echo "Copying \$i to \$par_eset_dir/"
+  cp -rL "\$i" "\$par_eset_dir/"
 done
 
+echo
+echo "Copying f_data files..."
+IFS=";" read -ra f_data <<<\$par_f_data
 for i in "\${f_data[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  echo "Copying \$i to \$par_f_data_dir/"
+  cp -rL "\$i" "\$par_f_data_dir/"
 done
 
+echo
+echo "Copying p_data files..."
+IFS=";" read -ra p_data <<<\$par_p_data
 for i in "\${p_data[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  echo "Copying \$i to \$par_p_data_dir/"
+  cp -rL "\$i" "\$par_p_data_dir/"
 done
 
-cp -rL "\$par_html_report" "\$par_output/"
+echo
+echo "Copying single files directly..."
+mkdir -p \$(dirname "\$par_html_report_output")
+echo "Copying \$par_html_report to \$par_html_report_output"
+cp -L "\$par_html_report" "\$par_html_report_output"
 
-cp -rL "\$par_run_params" "\$par_output/"
+echo "Copying \$par_run_params to \$par_run_params_output"
+mkdir -p \$(dirname "\$par_run_params_output")
+cp -L "\$par_run_params" "\$par_run_params_output"
+
+echo
+echo "Publishing completed successfully!"
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"
@@ -1512,8 +1747,29 @@ 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 "$VIASH_PAR_OUTPUT" ]; then
-    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
+  if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
+    VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_OUTPUT_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ]; then
+    VIASH_PAR_NRREADSNRGENESPERCHROM_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ]; then
+    VIASH_PAR_STAR_QC_METRICS_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_QC_METRICS_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_ESET_DIR" ]; then
+    VIASH_PAR_ESET_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_ESET_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_F_DATA_DIR" ]; then
+    VIASH_PAR_F_DATA_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_F_DATA_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_P_DATA_DIR" ]; then
+    VIASH_PAR_P_DATA_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_P_DATA_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
+    VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
+  fi
+  if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
+    VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_HTML_REPORT_OUTPUT")
   fi
   if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
     VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
@@ -1531,8 +1787,36 @@ fi
 
 
 # check whether required files exist
-if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
-  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
+if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
+  ViashError "Output file '$VIASH_PAR_STAR_OUTPUT_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && [ ! -e "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ]; then
+  ViashError "Output file '$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && [ ! -e "$VIASH_PAR_STAR_QC_METRICS_DIR" ]; then
+  ViashError "Output file '$VIASH_PAR_STAR_QC_METRICS_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_ESET_DIR" ] && [ ! -e "$VIASH_PAR_ESET_DIR" ]; then
+  ViashError "Output file '$VIASH_PAR_ESET_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_F_DATA_DIR" ] && [ ! -e "$VIASH_PAR_F_DATA_DIR" ]; then
+  ViashError "Output file '$VIASH_PAR_F_DATA_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_P_DATA_DIR" ] && [ ! -e "$VIASH_PAR_P_DATA_DIR" ]; then
+  ViashError "Output file '$VIASH_PAR_P_DATA_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
+  ViashError "Output file '$VIASH_PAR_RUN_PARAMS_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
 fi
 
diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml
index 0dade7f5..24e6f41d 100644
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -285,9 +285,9 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -317,7 +317,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/parallel_map/_viash.yaml b/target/executable/parallel_map/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/parallel_map/_viash.yaml
+++ b/target/executable/parallel_map/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map
index d64f1781..01d78d8a 100755
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -461,9 +461,9 @@ 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="2025-08-22T08:16:50Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml
index 73bb52bb..002387a3 100644
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -247,7 +247,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/report/create_report/_viash.yaml b/target/executable/report/create_report/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/report/create_report/_viash.yaml
+++ b/target/executable/report/create_report/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report
index 8e316592..3d02beb6 100755
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-08-22T08:16:50Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml
index 64ca0475..49f18298 100644
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -204,9 +204,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -236,7 +236,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/stats/combine_star_logs/_viash.yaml b/target/executable/stats/combine_star_logs/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/stats/combine_star_logs/_viash.yaml
+++ b/target/executable/stats/combine_star_logs/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs
index dc855967..24798c14 100755
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -457,9 +457,9 @@ 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="2025-08-22T08:16:48Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
index d74905b2..3e04f7af 100644
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -188,9 +188,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -220,7 +220,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/stats/generate_pool_statistics/_viash.yaml b/target/executable/stats/generate_pool_statistics/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/stats/generate_pool_statistics/_viash.yaml
+++ b/target/executable/stats/generate_pool_statistics/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
index 5d7e1b24..52e8f6fd 100755
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -458,9 +458,9 @@ 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="2025-08-22T08:16:50Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
index e935489a..2a12308e 100644
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -260,9 +260,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -292,7 +292,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/stats/generate_well_statistics/_viash.yaml b/target/executable/stats/generate_well_statistics/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/stats/generate_well_statistics/_viash.yaml
+++ b/target/executable/stats/generate_well_statistics/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics
index 88d18ea6..e41aa683 100755
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -458,9 +458,9 @@ 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="2025-08-22T08:16:48Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml
index b69b1063..e231837d 100644
--- a/target/executable/utils/save_params/.config.vsh.yaml
+++ b/target/executable/utils/save_params/.config.vsh.yaml
@@ -151,9 +151,9 @@ build_info:
   output: "target/executable/utils/save_params"
   executable: "target/executable/utils/save_params/save_params"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -183,7 +183,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/executable/utils/save_params/_viash.yaml b/target/executable/utils/save_params/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/executable/utils/save_params/_viash.yaml
+++ b/target/executable/utils/save_params/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params
index 88efbf39..7d50dba3 100755
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -453,9 +453,9 @@ 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="2025-08-22T08:16:50Z"
+LABEL org.opencontainers.image.created="2025-08-28T11:55:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+LABEL org.opencontainers.image.revision="fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
 LABEL org.opencontainers.image.version="add-eset-output-param"
 
 VIASHDOCKER
diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml
index 0d634b5d..813721f6 100644
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -206,9 +206,9 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -238,7 +238,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/eset/create_eset/_viash.yaml b/target/nextflow/eset/create_eset/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/eset/create_eset/_viash.yaml
+++ b/target/nextflow/eset/create_eset/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf
index b7a03107..edb342e7 100644
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,9 +3309,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3330,7 +3330,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml
index 6a3fe796..829e7ddc 100644
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -215,7 +215,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/eset/create_fdata/_viash.yaml b/target/nextflow/eset/create_fdata/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/eset/create_fdata/_viash.yaml
+++ b/target/nextflow/eset/create_fdata/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf
index 095319e8..91f508b0 100644
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,9 +3279,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3300,7 +3300,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml
index 55035940..db34488f 100644
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -197,9 +197,9 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -229,7 +229,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/eset/create_pdata/_viash.yaml b/target/nextflow/eset/create_pdata/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/eset/create_pdata/_viash.yaml
+++ b/target/nextflow/eset/create_pdata/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf
index f6b4d8f2..60277f33 100644
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,9 +3293,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3314,7 +3314,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index d1172349..8dffbacb 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -155,9 +155,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -187,7 +187,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
index 14226f7a..d5324a88 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,9 +3233,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3254,7 +3254,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index c25c3a1f..6ddfd196 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -164,9 +164,9 @@ 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: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -196,7 +196,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
index 89cb2640..a5909f31 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -3244,9 +3244,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3265,7 +3265,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
index b4e522b7..7baafb17 100644
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -139,9 +139,9 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -171,7 +171,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/io/publish_fastqs/_viash.yaml b/target/nextflow/io/publish_fastqs/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/io/publish_fastqs/_viash.yaml
+++ b/target/nextflow/io/publish_fastqs/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf
index 22088451..931a964c 100644
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,9 +3207,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3228,7 +3228,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml
index 23178dc8..9a0b94a1 100644
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -77,13 +77,90 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
-- name: "Output arguments"
+- name: "Output directory"
+  description: "Determines the name of output directories\n"
   arguments:
   - type: "file"
-    name: "--output"
+    name: "--star_output_dir"
     info: null
     default:
-    - "$id"
+    - "star_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--nrReadsNrGenesPerChrom_dir"
+    info: null
+    default:
+    - "nrReadsNrGenesPerChrom"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_qc_metrics_dir"
+    info: null
+    default:
+    - "starLogs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--eset_dir"
+    info: null
+    default:
+    - "esets"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--f_data_dir"
+    info: null
+    default:
+    - "fData"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--p_data_dir"
+    info: null
+    default:
+    - "pData"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output file arguments"
+  description: "Determines the name of output files"
+  arguments:
+  - type: "file"
+    name: "--run_params_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
     must_exist: true
     create_parent: true
     required: false
@@ -202,9 +279,9 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -234,7 +311,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/io/publish_results/_viash.yaml b/target/nextflow/io/publish_results/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/io/publish_results/_viash.yaml
+++ b/target/nextflow/io/publish_results/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf
index b6f954d3..6d517c36 100644
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3121,13 +3121,14 @@ meta = [
       ]
     },
     {
-      "name" : "Output arguments",
+      "name" : "Output directory",
+      "description" : "Determines the name of output directories\n",
       "arguments" : [
         {
           "type" : "file",
-          "name" : "--output",
+          "name" : "--star_output_dir",
           "default" : [
-            "$id"
+            "star_output"
           ],
           "must_exist" : true,
           "create_parent" : true,
@@ -3135,6 +3136,97 @@ meta = [
           "direction" : "output",
           "multiple" : false,
           "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--nrReadsNrGenesPerChrom_dir",
+          "default" : [
+            "nrReadsNrGenesPerChrom"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--star_qc_metrics_dir",
+          "default" : [
+            "starLogs"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--eset_dir",
+          "default" : [
+            "esets"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--f_data_dir",
+          "default" : [
+            "fData"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--p_data_dir",
+          "default" : [
+            "pData"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    },
+    {
+      "name" : "Output file arguments",
+      "description" : "Determines the name of output files",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--run_params_output",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--html_report_output",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
         }
       ]
     }
@@ -3277,9 +3369,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3298,7 +3390,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
@@ -3342,7 +3434,14 @@ $( 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 ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; 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 )
+$( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_eset_dir='&'#" ; else echo "# par_eset_dir="; fi )
+$( 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 ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${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 )
 $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -3365,48 +3464,97 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 ## VIASH END
 #!/bin/bash
 
-echo "Publishing \\$par_input -> \\$par_output"
+set -eo pipefail
+
+echo "Publishing results to multiple output directories"
+
+# Create output directories for multiple files
+echo "Creating output directories..."
+
+path_pars=(
+  par_star_output_dir
+  par_nrReadsNrGenesPerChrom_dir
+  par_star_qc_metrics_dir
+  par_eset_dir
+  par_f_data_dir
+  par_p_data_dir
+  par_html_report_output
+  par_run_params_output
+)
+
+for par in \\${path_pars[@]}; do
+    curr_val="\\${!par}"
+    new_value=\\$(realpath --canonicalize-missing "\\$curr_val")
+    declare -g "\\$par=\\$new_value"
+done
+
+mkdir -p "\\$par_star_output_dir" && echo "\\$par_star_output_dir created"
+mkdir -p "\\$par_nrReadsNrGenesPerChrom_dir" && echo "\\$par_nrReadsNrGenesPerChrom_dir created"  
+mkdir -p "\\$par_star_qc_metrics_dir" && echo "\\$par_star_qc_metrics_dir created"
+mkdir -p "\\$par_eset_dir" && echo "\\$par_eset_dir created"
+mkdir -p "\\$par_f_data_dir" && echo "\\$par_f_data_dir created"
+mkdir -p "\\$par_p_data_dir" && echo "\\$par_p_data_dir created"
 
 echo
-echo "Creating directory if it does not exist:"
-mkdir -p "\\$par_output" && echo "\\$par_output created"
-
-echo
-echo "Copying files..."
+echo "Copying STAR output files..."
 IFS=";" read -ra star_output <<<\\$par_star_output
-IFS=";" read -ra nrReadsNrGenesPerChrom <<<\\$par_nrReadsNrGenesPerChrom
-IFS=";" read -ra star_qc_metrics <<<\\$par_star_qc_metrics
-IFS=";" read -ra eset <<<\\$par_eset
-IFS=";" read -ra f_data <<<\\$par_f_data
-IFS=";" read -ra p_data <<<\\$par_p_data
-
 for i in "\\${star_output[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  echo "Copying \\$i to \\$par_star_output_dir/"
+  cp -rL "\\$i" "\\$par_star_output_dir/"
 done
 
+echo
+echo "Copying nrReadsNrGenesPerChrom files..."
+IFS=";" read -ra nrReadsNrGenesPerChrom <<<\\$par_nrReadsNrGenesPerChrom
 for i in "\\${nrReadsNrGenesPerChrom[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  echo "Copying \\$i to \\$par_nrReadsNrGenesPerChrom_dir/"
+  cp -rL "\\$i" "\\$par_nrReadsNrGenesPerChrom_dir/"
 done
 
+echo
+echo "Copying STAR QC metrics files..."
+IFS=";" read -ra star_qc_metrics <<<\\$par_star_qc_metrics
 for i in "\\${star_qc_metrics[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  echo "Copying \\$i to \\$par_star_qc_metrics_dir/"
+  cp -rL "\\$i" "\\$par_star_qc_metrics_dir/"
 done
 
+echo
+echo "Copying eset files..."
+IFS=";" read -ra eset <<<\\$par_eset
 for i in "\\${eset[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  echo "Copying \\$i to \\$par_eset_dir/"
+  cp -rL "\\$i" "\\$par_eset_dir/"
 done
 
+echo
+echo "Copying f_data files..."
+IFS=";" read -ra f_data <<<\\$par_f_data
 for i in "\\${f_data[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  echo "Copying \\$i to \\$par_f_data_dir/"
+  cp -rL "\\$i" "\\$par_f_data_dir/"
 done
 
+echo
+echo "Copying p_data files..."
+IFS=";" read -ra p_data <<<\\$par_p_data
 for i in "\\${p_data[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  echo "Copying \\$i to \\$par_p_data_dir/"
+  cp -rL "\\$i" "\\$par_p_data_dir/"
 done
 
-cp -rL "\\$par_html_report" "\\$par_output/"
+echo
+echo "Copying single files directly..."
+mkdir -p \\$(dirname "\\$par_html_report_output")
+echo "Copying \\$par_html_report to \\$par_html_report_output"
+cp -L "\\$par_html_report" "\\$par_html_report_output"
 
-cp -rL "\\$par_run_params" "\\$par_output/"
+echo "Copying \\$par_run_params to \\$par_run_params_output"
+mkdir -p \\$(dirname "\\$par_run_params_output")
+cp -L "\\$par_run_params" "\\$par_run_params_output"
+
+echo
+echo "Publishing completed successfully!"
 VIASHMAIN
 bash "$tempscript"
 '''
diff --git a/target/nextflow/io/publish_results/nextflow_schema.json b/target/nextflow/io/publish_results/nextflow_schema.json
index b438683b..b83eb8e6 100644
--- a/target/nextflow/io/publish_results/nextflow_schema.json
+++ b/target/nextflow/io/publish_results/nextflow_schema.json
@@ -85,17 +85,73 @@
         }
       }
     },
-    "output arguments": {
-      "title": "Output arguments",
+    "output directory": {
+      "title": "Output directory",
       "type": "object",
-      "description": "No description",
+      "description": "Determines the name of output directories\n",
       "properties": {
-        "output": {
+        "star_output_dir": {
           "type": "string",
           "format": "path",
           "description": "",
-          "help_text": "Type: `file`, multiple: `False`, default: `\"$id\"`, direction: `output`. ",
-          "default": "$id"
+          "help_text": "Type: `file`, multiple: `False`, default: `\"star_output\"`, direction: `output`. ",
+          "default": "star_output"
+        },
+        "nrReadsNrGenesPerChrom_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"nrReadsNrGenesPerChrom\"`, direction: `output`. ",
+          "default": "nrReadsNrGenesPerChrom"
+        },
+        "star_qc_metrics_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"starLogs\"`, direction: `output`. ",
+          "default": "starLogs"
+        },
+        "eset_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"esets\"`, direction: `output`. ",
+          "default": "esets"
+        },
+        "f_data_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"fData\"`, direction: `output`. ",
+          "default": "fData"
+        },
+        "p_data_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"pData\"`, direction: `output`. ",
+          "default": "pData"
+        }
+      }
+    },
+    "output file arguments": {
+      "title": "Output file arguments",
+      "type": "object",
+      "description": "Determines the name of output files",
+      "properties": {
+        "run_params_output": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_params_output\"`, direction: `output`. ",
+          "default": "$id.$key.run_params_output"
+        },
+        "html_report_output": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.html_report_output\"`, direction: `output`. ",
+          "default": "$id.$key.html_report_output"
         }
       }
     },
@@ -117,7 +173,10 @@
       "$ref": "#/$defs/input arguments"
     },
     {
-      "$ref": "#/$defs/output arguments"
+      "$ref": "#/$defs/output directory"
+    },
+    {
+      "$ref": "#/$defs/output file arguments"
     },
     {
       "$ref": "#/$defs/nextflow input-output arguments"
diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml
index 94b23ba2..7e7416e8 100644
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -285,9 +285,9 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -317,7 +317,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/parallel_map/_viash.yaml b/target/nextflow/parallel_map/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/parallel_map/_viash.yaml
+++ b/target/nextflow/parallel_map/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf
index f4790ee4..3db74190 100644
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,9 +3379,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3400,7 +3400,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml
index fe5fcaac..2e8a3a49 100644
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -247,7 +247,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/report/create_report/_viash.yaml b/target/nextflow/report/create_report/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/report/create_report/_viash.yaml
+++ b/target/nextflow/report/create_report/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf
index a033ed68..7a9a65bb 100644
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3323,9 +3323,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3344,7 +3344,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
index 981ed587..05e913d8 100644
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -204,9 +204,9 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -236,7 +236,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/stats/combine_star_logs/_viash.yaml b/target/nextflow/stats/combine_star_logs/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/stats/combine_star_logs/_viash.yaml
+++ b/target/nextflow/stats/combine_star_logs/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf
index b3aaa854..2f38c0d5 100644
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,9 +3295,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3316,7 +3316,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
index e9f37143..a4aabaa3 100644
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -188,9 +188,9 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -220,7 +220,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/stats/generate_pool_statistics/_viash.yaml b/target/nextflow/stats/generate_pool_statistics/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/stats/generate_pool_statistics/_viash.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf
index eca0e4dc..13675516 100644
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,9 +3279,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3300,7 +3300,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
index 01f69741..177446bc 100644
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -260,9 +260,9 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -292,7 +292,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/stats/generate_well_statistics/_viash.yaml b/target/nextflow/stats/generate_well_statistics/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/stats/generate_well_statistics/_viash.yaml
+++ b/target/nextflow/stats/generate_well_statistics/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf
index ab3cea7f..c325d718 100644
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3361,9 +3361,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3382,7 +3382,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml
index bfeb6211..7917d735 100644
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -160,9 +160,9 @@ build_info:
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
 package_config:
@@ -194,7 +194,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/utils/concatRuns/_viash.yaml b/target/nextflow/utils/concatRuns/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/utils/concatRuns/_viash.yaml
+++ b/target/nextflow/utils/concatRuns/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf
index 3934c56f..a0bf853f 100644
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,9 +3229,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3250,7 +3250,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml
index 90e56757..ae45b29c 100644
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -169,9 +169,9 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -201,7 +201,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/utils/listInputDir/_viash.yaml b/target/nextflow/utils/listInputDir/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/utils/listInputDir/_viash.yaml
+++ b/target/nextflow/utils/listInputDir/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf
index 23e3f787..d908fc9a 100644
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3236,9 +3236,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3257,7 +3257,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml
index 2e1ef083..b091febf 100644
--- a/target/nextflow/utils/save_params/.config.vsh.yaml
+++ b/target/nextflow/utils/save_params/.config.vsh.yaml
@@ -151,9 +151,9 @@ build_info:
   output: "target/nextflow/utils/save_params"
   executable: "target/nextflow/utils/save_params/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -183,7 +183,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/utils/save_params/_viash.yaml b/target/nextflow/utils/save_params/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/utils/save_params/_viash.yaml
+++ b/target/nextflow/utils/save_params/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf
index 192697e7..04c39d7f 100644
--- a/target/nextflow/utils/save_params/main.nf
+++ b/target/nextflow/utils/save_params/main.nf
@@ -3223,9 +3223,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/utils/save_params",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3244,7 +3244,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
index 362e3a99..77e92444 100644
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -345,9 +345,9 @@ build_info:
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
   - "target/nextflow/stats/generate_pool_statistics"
@@ -390,7 +390,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/workflows/htrnaseq/_viash.yaml b/target/nextflow/workflows/htrnaseq/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/workflows/htrnaseq/_viash.yaml
+++ b/target/nextflow/workflows/htrnaseq/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf
index 1e81c6fe..ce6e6982 100644
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3484,9 +3484,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3505,7 +3505,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
@@ -3893,7 +3893,6 @@ workflow run_wf {
       | setState([
         "star_output": "star_output",
         "fastq_output": "fastq_output_directory",
-        "star_output": "star_output",
         "nrReadsNrGenesPerChrom": "nrReadsNrGenesPerChromPool",
         "star_qc_metrics": "star_qc_metrics",
         "eset": "eset",
diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml
index 08d17c06..7dbbf8d8 100644
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -124,7 +124,40 @@ argument_groups:
 - name: "Output arguments"
   arguments:
   - type: "file"
-    name: "--eset_output"
+    name: "--star_output_dir"
+    info: null
+    default:
+    - "star_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--nrReadsNrGenesPerChrom_dir"
+    info: null
+    default:
+    - "nrReadsNrGenesPerChrom"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_qc_metrics_dir"
+    info: null
+    default:
+    - "starLogs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--eset_dir"
     info: null
     default:
     - "esets"
@@ -134,11 +167,35 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--f_data_dir"
+    info: null
+    default:
+    - "fData"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--p_data_dir"
+    info: null
+    default:
+    - "pData"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "nextflow_script"
   path: "main.nf"
   is_executable: true
   entrypoint: "run_wf"
+- type: "file"
+  path: "disable_publishfiles_process.config"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -239,6 +296,7 @@ runners:
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
     script:
+    - "includeConfig(\"disable_publishfiles_process.config\")"
     - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
@@ -254,9 +312,9 @@ build_info:
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
   dependencies:
   - "target/nextflow/utils/listInputDir"
   - "target/nextflow/workflows/htrnaseq"
@@ -292,7 +350,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/workflows/runner/_viash.yaml b/target/nextflow/workflows/runner/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/workflows/runner/_viash.yaml
+++ b/target/nextflow/workflows/runner/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/workflows/runner/disable_publishfiles_process.config b/target/nextflow/workflows/runner/disable_publishfiles_process.config
new file mode 100644
index 00000000..6cff5e26
--- /dev/null
+++ b/target/nextflow/workflows/runner/disable_publishfiles_process.config
@@ -0,0 +1,5 @@
+process {
+  withName: publishFilesProc {
+    publishDir = [ enabled: false ]
+  }
+}
\ No newline at end of file
diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf
index 83704ba1..dc6516dd 100644
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3173,7 +3173,46 @@ meta = [
       "arguments" : [
         {
           "type" : "file",
-          "name" : "--eset_output",
+          "name" : "--star_output_dir",
+          "default" : [
+            "star_output"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--nrReadsNrGenesPerChrom_dir",
+          "default" : [
+            "nrReadsNrGenesPerChrom"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--star_qc_metrics_dir",
+          "default" : [
+            "starLogs"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--eset_dir",
           "default" : [
             "esets"
           ],
@@ -3183,6 +3222,32 @@ meta = [
           "direction" : "output",
           "multiple" : false,
           "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--f_data_dir",
+          "default" : [
+            "fData"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--p_data_dir",
+          "default" : [
+            "pData"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
         }
       ]
     }
@@ -3194,6 +3259,10 @@ meta = [
       "is_executable" : true,
       "entrypoint" : "run_wf"
     },
+    {
+      "type" : "file",
+      "path" : "disable_publishfiles_process.config"
+    },
     {
       "type" : "file",
       "path" : "/src/config/labels.config",
@@ -3325,6 +3394,7 @@ meta = [
           "cpu1000" : "cpus = 1000"
         },
         "script" : [
+          "includeConfig(\\"disable_publishfiles_process.config\\")",
           "includeConfig(\\"nextflow_labels.config\\")"
         ]
       },
@@ -3348,9 +3418,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3369,7 +3439,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
@@ -3432,7 +3502,6 @@ workflow run_wf {
         def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states]
         return [new_id, new_state]
       }
-
       | save_params.run(
         key: "save_params_runner",
         fromState: {id, state ->
@@ -3466,6 +3535,19 @@ workflow run_wf {
       )
     
     htrnaseq_ch = input_ch
+      | map { id, state -> 
+        // The argument names for this workflow and the htrnaseq workflow may overlap
+        // here, we store a copy in order to make sure to not accidentally overwrite the state.
+        def new_state = state + [
+          "star_output_dir_workflow": state.star_output_dir,
+          "nrReadsNrGenesPerChrom_dir_workflow": state.nrReadsNrGenesPerChrom_dir,
+          "star_qc_metrics_dir_workflow": state.star_qc_metrics_dir,
+          "eset_dir_workflow": state.eset_dir,
+          "f_data_dir_workflow": state.f_data_dir,
+          "p_data_dir_workflow": state.p_data_dir
+        ]
+        return [id, new_state]
+      }
       | listInputDir.run(
         fromState: [
           "input": "input",
@@ -3525,49 +3607,81 @@ workflow run_wf {
         toState: { id, result, state -> state + result }
       )
 
-      // The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
-      // but for publishing the results, this is not handy because we want to use the $id
-      // variable as a pointer to the target data.
-      //
-      // So, we should combine everything together
-      //
-      // project_id / experiment_id / "data_processed" / date_workflow
-    grouped_ch = htrnaseq_ch
-      | toSortedList
-      | map{ vs ->
-          def all_fastqs
-          [
-            vs[0][1].run_id, // The original ID
-            [
-              star_output: reduce_paths(vs.collect{ it[1].star_output }.flatten()),
-              nrReadsNrGenesPerChrom: reduce_paths(vs.collect{ it[1].nrReadsNrGenesPerChrom }),
-              star_qc_metrics: reduce_paths(vs.collect{ it[1].star_qc_metrics }),
-              eset: reduce_paths(vs.collect{ it[1].eset }),
-              f_data: reduce_paths(vs.collect{ it[1].f_data }),
-              p_data: reduce_paths(vs.collect{ it[1].p_data }),
-              fastq_output: vs.collect{ it[1].fastq_output }.flatten().unique(),
-              html_report: vs.collect{ it[1].html_report }[0],  // The report is for all pools
-              plain_output: vs.collect{ it[1].plain_output }[0],
-              project_id: vs.collect{ it[1].project_id }[0],
-              experiment_id: vs.collect{ it[1].experiment_id }[0]
-            ]
-          ]
-        }
-
-    grouped_with_params_list_ch = grouped_ch.combine(save_params_ch)
+    // The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
+    // but for publishing the results, this is not handy because we want to use the $id
+    // variable as a pointer to the target data.
+    // So, we should combine everything together
+    results_publish_ch = htrnaseq_ch
+      | combine(save_params_ch)
       | map {new_id, grouped_ch_state, save_params_id, save_params_state ->
         def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
         return [new_id, new_state]
-      
       }
+      | toSortedList
+      | map{ vs ->
+          def states = vs.collect{it[1]}
 
-    results_publish_ch = grouped_with_params_list_ch
+          // The STAR output is a directory for each well in a plate (or pool of plates).
+          // The wells are grouped into a directory per sample. The name of this directory should
+          // match the sample_id.
+          def star_output_samples = states.collectMany{state -> 
+            state.star_output.collect{
+              def star_sample_dir = it.parent
+              assert star_sample_dir.name == state.sample_id: "Unexpected state: the parent directory of STAR output \
+                path '${it}' should match with the sample ID ${sample_id}"
+              star_sample_dir
+            }
+          }
+          def new_state = [
+            "star_output": star_output_samples,
+          ]
+
+          // Keys for which the values should be the same across samples
+          def state_keys_unique = [
+            "html_report",
+            "project_id",
+            "experiment_id",
+            "star_output_dir_workflow",
+            "nrReadsNrGenesPerChrom_dir_workflow",
+            "star_qc_metrics_dir_workflow",
+            "eset_dir_workflow",
+            "f_data_dir_workflow",
+            "p_data_dir_workflow",
+            "f_data",
+            "run_params"
+          ]
+          def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name ->
+            argument_values = states.collect{it.get(argument_name)}.unique()
+            assert argument_values.size() == 1, "State error: values for argument $argument_name should be the same across states. \
+                                                 Argument values: $argument_values"
+            // take the unique value from the set (there is only one)
+            def argument_value
+            argument_values.each { argument_value = it }
+            state_to_update + [(argument_name): argument_value]
+          }
+
+          // Keys that just require gathering of values across samples
+          def state_keys_collect = [
+            "nrReadsNrGenesPerChrom",
+            "star_qc_metrics",
+            "eset",
+            "p_data",
+          ]
+          def state_collect = state_keys_collect.collectEntries{ key_ ->
+            [key_, states.collect{it.get(key_)}]
+          }
+
+          new_state = new_state + state_unique_keys + state_collect
+          [states[0].run_id, new_state]  
+      }
       | publish_results.run(
         fromState: { id, state ->
-          def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
-          println("Publising results to ${params.results_publish_dir}/${output_dir}")
+          def prefix = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
 
-          [
+          println("Publising results to ${params.results_publish_dir}/${prefix}")
+
+          [ 
+            // Inputs
             star_output: state.star_output,
             nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom,
             star_qc_metrics: state.star_qc_metrics,
@@ -3576,10 +3690,18 @@ workflow run_wf {
             p_data: state.p_data,
             html_report: state.html_report,
             run_params: state.run_params,
-            output: output_dir.toString()
+            // Output locations
+            run_params_output: "${prefix}/${state.run_params.name}",
+            html_report_output: "${prefix}/${state.html_report.name}", 
+            star_output_dir: "${prefix}/${state.star_output_dir_workflow}",
+            nrReadsNrGenesPerChrom_dir: "${prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}",
+            star_qc_metrics_dir: "${prefix}/${state.star_qc_metrics_dir_workflow}",
+            eset_dir: "${prefix}/${state.eset_dir_workflow}",
+            f_data_dir: "${prefix}/${state.f_data_dir_workflow}",
+            p_data_dir: "${prefix}/${state.p_data_dir_workflow}"
           ]
         },
-        toState: { id, result, state -> state + ["eset_output": state.eset] },
+        toState: { id, result, state -> result },
         directives: [
           publishDir: [
             path: "${params.results_publish_dir}", 
@@ -3588,33 +3710,43 @@ workflow run_wf {
           ]
         ]
       )
+      | setState([
+          "star_output_dir",
+          "nrReadsNrGenesPerChrom_dir",
+          "star_qc_metrics_dir",
+          "eset_dir",
+          "f_data_dir",
+          "p_data_dir",
+        ]
+      )
 
-    fastq_publish_ch = grouped_ch
-      | flatMap{id, state ->
-        def new_states = state.fastq_output.collect{fastq_dir -> 
-          def run_id = fastq_dir.name // The folder name corresponds to the run
-          def sample = fastq_dir.parent.name // The parent folder name should be the sample
-          def new_id = "${run_id}/${sample}"
-          def fastq_files = fastq_dir.listFiles()
-          def new_state = [
-            "fastq_output": fastq_files,
-            "sample_id": sample,
-            "run_id": run_id 
-          ]
-          return [new_id, new_state]
-        }
-        return new_states
+    fastq_publish_ch = htrnaseq_ch
+      // The output from the htrnaseq workflow is on sample (i.e. pool) level
+      // Multiple sequencing runs may have contributes to the FASTQ files from this pool.
+      // So the fastq_output is a list of directories, one for each run.
+      // We assume that the names of the folders containing the FASTQ files are equal to the pool names.
+      | flatMap {id, state ->
+          state.fastq_output.collect{fastq_dir ->
+            def run_id = fastq_dir.name
+            def new_id = "${run_id}/${state.sample_id}"
+            def new_state = [
+              "fastq_output": fastq_dir.listFiles(),
+              "sample_id": state.sample_id,
+              "run_id": run_id,
+              "output": "${run_id}/${date}_htrnaseq_${version}/${state.sample_id}".toString()
+            ]
+            [new_id, new_state]
+          }
       }
+      // A folder containing the FASTQ files from a certain pool may be present in the state from
+      // multiple samples; if that pool contributed to the data from those samples.
+      // Those FASTQ files will only be published once by filtering out the duplicate events here.
+      | unique{it[0]}
       | publish_fastqs.run(
-        fromState: { id, state ->
-          def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
-          println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}")
-
-          [
-            input: state.fastq_output,
-            output: output_dir.toString(),
-          ]
-        },
+        fromState: [
+          "input": "fastq_output",
+          "output": "output",
+        ],
         toState: { id, result, state -> state },
         directives: [
           publishDir: [
@@ -3625,12 +3757,9 @@ workflow run_wf {
         ]
       )
 
-    output_ch = results_publish_ch
-      | setState(["eset_output"])
-
   emit:
-    grouped_ch
-      | map{ id, state -> [ id, [ _meta: [ join_id: state.run_id ] ] ] }
+    results_publish_ch
+
 }
 
 def get_version(inputFile) {
@@ -3641,39 +3770,6 @@ def get_version(inputFile) {
   return version
 }
 
-/*
- * This function uses a heuristic to group a list of paths so that the level of nesting
- * of IDs is represented in the output.
- *
- * We iterative of the path sections (subfolders) from the last (file) the first (root node).
- * The first path segment that is common across all 'events' is the cutoff. We cutoff the paths
- * at this level, select the unique elements from the list and use that as input for the next step.
- *
- * An optional offset allows one to shift the cutoff left or right.
- */
-def reduce_paths(paths, offset = 0) {
-  def path_length = paths.collect{ it.getNameCount() }[0]
-
-  def unique_list = (path_length-1..0).collectEntries { i ->
-    [ (i): paths.collect{ it.getName(i) }.unique().size() ]
-  }
-
-  def cutoff = unique_list.find{ it.value == 1 }.key
-
-  def grouped_paths = paths.collect{ f -> "/" + f.subpath(0, cutoff+1+offset) }.unique()
-
-  println("")
-  println("Detecting the common path section to pass to the next step:")
-  print("  From: ")
-  print paths
-  println("")
-  print("  To:   ")
-  print grouped_paths
-  println("")
-
-  return grouped_paths
-}
-
 // inner workflow hook
 def innerWorkflowFactory(args) {
   return run_wf
diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config
index e1d51c85..d8d759e2 100644
--- a/target/nextflow/workflows/runner/nextflow.config
+++ b/target/nextflow/workflows/runner/nextflow.config
@@ -122,4 +122,5 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
+includeConfig("disable_publishfiles_process.config")
 includeConfig("nextflow_labels.config")
diff --git a/target/nextflow/workflows/runner/nextflow_schema.json b/target/nextflow/workflows/runner/nextflow_schema.json
index 2d11695b..bbd4c521 100644
--- a/target/nextflow/workflows/runner/nextflow_schema.json
+++ b/target/nextflow/workflows/runner/nextflow_schema.json
@@ -104,12 +104,47 @@
       "type": "object",
       "description": "No description",
       "properties": {
-        "eset_output": {
+        "star_output_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"star_output\"`, direction: `output`. ",
+          "default": "star_output"
+        },
+        "nrReadsNrGenesPerChrom_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"nrReadsNrGenesPerChrom\"`, direction: `output`. ",
+          "default": "nrReadsNrGenesPerChrom"
+        },
+        "star_qc_metrics_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"starLogs\"`, direction: `output`. ",
+          "default": "starLogs"
+        },
+        "eset_dir": {
           "type": "string",
           "format": "path",
           "description": "",
           "help_text": "Type: `file`, multiple: `False`, default: `\"esets\"`, direction: `output`. ",
           "default": "esets"
+        },
+        "f_data_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"fData\"`, direction: `output`. ",
+          "default": "fData"
+        },
+        "p_data_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"pData\"`, direction: `output`. ",
+          "default": "pData"
         }
       }
     },
diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
index d7507ae2..6bee00c3 100644
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
   output: "target/nextflow/workflows/well_demultiplex"
   executable: "target/nextflow/workflows/well_demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt"
   - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
@@ -258,7 +258,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/workflows/well_demultiplex/_viash.yaml b/target/nextflow/workflows/well_demultiplex/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/workflows/well_demultiplex/_viash.yaml
+++ b/target/nextflow/workflows/well_demultiplex/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf
index 056fefdd..38c77c20 100644
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3327,9 +3327,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3348,7 +3348,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"
diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
index 256ec479..3362f491 100644
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
   output: "target/nextflow/workflows/well_metadata"
   executable: "target/nextflow/workflows/well_metadata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53"
+  git_commit: "fdbd9fce90c65c9d7cd1f09286cc9266593ae203"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-15-gd3962a3"
+  git_tag: "v0.7.2-23-gfdbd9fc"
 package_config:
   name: "htrnaseq"
   version: "add-eset-output-param"
@@ -247,7 +247,7 @@ package_config:
   target: "target"
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
-    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ += '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\" }"
diff --git a/target/nextflow/workflows/well_metadata/_viash.yaml b/target/nextflow/workflows/well_metadata/_viash.yaml
index 26386aa1..31895a6c 100644
--- a/target/nextflow/workflows/well_metadata/_viash.yaml
+++ b/target/nextflow/workflows/well_metadata/_viash.yaml
@@ -14,7 +14,7 @@ info:
       dest: resources_test
 config_mods: |
   .requirements.commands := ['ps']
-  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
   .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
 version: add-eset-output-param
diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf
index 9b9e3014..25407b50 100644
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,9 +3299,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_metadata",
     "viash_version" : "0.9.4",
-    "git_commit" : "d3962a3f0ce0399d6d0ad37b9a30f682787e8a53",
+    "git_commit" : "fdbd9fce90c65c9d7cd1f09286cc9266593ae203",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-15-gd3962a3"
+    "git_tag" : "v0.7.2-23-gfdbd9fc"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3320,7 +3320,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".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",
+      ".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 := 'add-eset-output-param'"