Build branch v0.3 with version v0.3.11 (cd2cfac)

Build pipeline: viash-hub.demultiplex.v0.3-nwj5p Source commit: cd2cfac18e Source message: Bump version to v0.3.11
Build branch v0.3 with version v0.3.10 (e6fbd0c)
2025-05-14 09:11:58 +00:00 · 2025-05-07 11:35:04 +00:00
48 changed files with 886 additions and 222 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,15 @@
+# demultiplex v0.3.11
+
+# New features
+
+* Output demultiplexer logs and metrics (PR #41).
+
+# demultiplex v0.3.10
+
+## Minor changes
+
+* Moved the test resources to their new location (PR #37).
+
 # demultiplex v0.3.9

 ## Bug fixes
--- a/README.md
+++ b/README.md
@@ -1,6 +1,10 @@
+
+
 # Demultiplex.vsh

-Demultiplex.vsh is a workflow for demultiplexing of raw sequencing data. Currently data from Illumina and Element Biosciences sequencers are supported.
+Demultiplex.vsh is a workflow for demultiplexing of raw sequencing data.
+Currently data from Illumina and Element Biosciences sequencers are
+supported.

 [![ViashHub](https://img.shields.io/badge/ViashHub-demultiplex-7a4baa.svg)](https://web.viash-hub.com/packages/demultiplex)
 [![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fdemultiplex-blue.svg)](https://github.com/viash-hub/demultiplex)
@@ -11,90 +15,205 @@ Issues](https://img.shields.io/github/issues/viash-hub/demultiplex.svg)](https:/
 [![Viash
 version](https://img.shields.io/badge/Viash-v0.9.4-blue)](https://viash.io)

+## Introcuction
+
+This workflow is designed to demultiplex raw RNA-seq sequencing data
+from Illumina and Element Biosciences sequencers.
+
+The workflow is built in a modular fashion, where most of the base
+functionality is provided by components from
+[`biobox`](https://www.viash-hub.com/packages/biobox/latest)
+supplemented by custom base components and workflow components in this
+package. Each of these components can be used independently as
+stand-alone modules with a standardized interface.
+
+The full workflow can be run in two ways:
+
+1.  Run the [main
+    workflow](https://www.viash-hub.com/packages/demultiplex/v0.3.4/components/demultiplex)
+    containing the main functionality.
+2.  Run the [(opinianated)
+    `runner`](https://www.viash-hub.com/packages/demultiplex/v0.3.4/components/runner)
+    where a number of choices (input/output structure and location) have
+    been made.
+
 ## Workflow Overview
-The workflow executes the following steps: 
-1. Unpacking the input data (when a TAR archive is provided)
-2. Run `bclconvert` or `bases2fastq`
-3. Run `falco` and convert Illumina InterOp information to csv
-4. Run `multiqc` to generate a report

-## Usage
+The workflow executes the following steps:

-Two variants of the same workflow are provided, depending on the flexibility in the ouput structure required:
+1.  Unpacking the input data (when a TAR archive is provided)
+2.  Run `bclconvert` or `bases2fastq`
+3.  Run `falco` and convert Illumina InterOp information to csv
+4.  Run `multiqc` to generate a report

-* The `runner` workflow provides a predifined output structure. It requires the minimal amount of parameters to be provided, at the cost of being less flexible. It is located at `target/nextflow/runner/main.nf`
-* The `demultiplex` workflow (`target/nextflow/demultiplex/main.nf`) allows for more fine-grained tuning, but required more parameters to be provided.
+## Example usage
+
+Two variants of the same workflow are provided, depending on the
+flexibility in the ouput structure required:
+
+- The `runner` workflow provides a predifined output structure. It
+  requires the minimal amount of parameters to be provided, at the cost
+  of being less flexible. It is located at
+  `target/nextflow/runner/main.nf`
+- The `demultiplex` workflow (`target/nextflow/demultiplex/main.nf`)
+  allows for more fine-grained tuning, but required more parameters to
+  be provided.

 ### Test data

-We have provided test data at `gs://viash-hub-test-data/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2`, but please feel free to bring your own. The URL of the test data can be provided as-is to the workflow, or you can download everything and specify a local path.
+We have provided test data at
+`gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2`
+(Illumina), but please feel free to bring your own. The URL of the test
+data can be provided as-is to the workflow, or you can download
+everything and specify a local path.
+
+The input data should follow the structure of either Illumina or Element
+Biosciences sequencers. The workflow will automatically detect which
+demultiplexer to use (`bclconvert` or `bases2fastq`) based on the
+presence of either `SampleSheet.csv` or `RunParameters.xml` in the input
+directory. Demultiplexer can also be set explicitly using the
+`--demultiplexer` parameter.

 ### Setup

-In order to use the workflows in this package, you'll need to do the following:
-* Install [nextflow](https://www.nextflow.io/docs/latest/install.html)
-* Install a nextflow compatible executor. This workflow provides a profile for [docker](https://docs.docker.com/get-started/).
+In order to use the workflows in this package, you’ll need to do the
+following:
+
+- Install [nextflow](https://www.nextflow.io/docs/latest/install.html)
+- Install a nextflow compatible executor. This workflow provides a
+  profile for [docker](https://docs.docker.com/get-started/).
+
+### Run from Viash Hub
+
+1.  Open [Viash Hub](https://www.viash-hub.com) and browse to the
+    [demultiplex
+    component](https://www.viash-hub.com/packages/demultiplex/v0.3.4/components/demultiplex).
+    Press the ‘Launch’ button and follow the instructions.
+
+![](assets/demultiplex-launch-small.png)
+
+2.  We will start an example run and set profile to `docker`.
+
+![](assets/demultiplex-launch-parameters-1.png)
+
+3.  In the next step, we provide the paramters as follows and leave the
+    rest as defalut:
+
+- `input`:
+  `gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2`
+
+![](assets/demultiplex-launch-parameters-2.png)
+
+Press the ‘Launch’ button at the end to get the instructions on how to
+run the workflow from the CLI.
+
+### Run using NF-Tower / Seqera Cloud
+
+It’s possible to run the workflow directly from [Seqera
+Cloud](https://cloud.seqera.io). The necessary [Nextflow schema
+file](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/)
+has been built and provided with the workflows in order to use the
+form-based input.
+
+1.  Select the option to run the workflow using Seqera Cloud. You will
+    need to create an API token for your account. Once this token is
+    filled in in the corresponding field, we will get the option to
+    select a ‘Workspace’ and a ‘Compute environment’.
+
+![](assets/demultiplex-launch-parameters-3.png)
+
+2.  Provide the parameters similar to the previous step.
+
+3.  In the next screen, pressing the ‘Launch’ button will actually start
+    the workflow on Seqera Cloud. A message is shown when the submit was
+    successful.
+
+![](assets/demultiplex-launch-parameters-4.png)

 ### Setting up SCM

-In order to let nextflow use the viash-hub workflows, you need to setup a [SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) file. This can be done once by creating `$HOME/.nextflow/scm` and adding the following:
-```
-providers {
-   vsh {
-    platform = 'gitlab'
-    server = "packages.viash-hub.com"
-  }
-}
-```
+In order to let nextflow use the viash-hub workflows, you need to setup
+a [SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration)
+file. This can be done once by creating `$HOME/.nextflow/scm` and adding
+the following:

-Alternatively, a custom location for the SCM file can be specified using the `NXF_SCM_FILE` environment variable.
+    providers {
+       vsh {
+        platform = 'gitlab'
+        server = "packages.viash-hub.com"
+      }
+    }

-You can check if everything is working by getting the `--help` for a workflow:
-```bash
+Alternatively, a custom location for the SCM file can be specified using
+the `NXF_SCM_FILE` environment variable.
+
+You can check if everything is working by getting the `--help` for a
+workflow:
+
+``` bash
 nextflow run \
 vsh/demultiplex \
-r v0.3.9 \
+-r v0.3.11 \
 --help
 ```

+### Run from the CLI
+
+Running from the CLI directly without using Viash hub is possible as
+well. The easiest is to use the integrated help functionality, for
+instance using the following:
+
+``` bash
+ nextflow run vsh/demultiplex \
+  -revision v0.3.11 \
+  -main-script target/nextflow/workflows/runner/main.nf \
+  --help
+```
+
+Having this project available locally, you can run the following
+command:
+
+``` bash
+nextflow run vsh/demultiplex \
+-r v0.3.11 \
+-main-script target/nextflow/runner/main.nf \
+--input "gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2"  \
+--demultiplexer bclconvert \
+--skip_copycomplete_check \
+--publish_dir example_output/ \
+-profile docker \
+-c src/config/labels.config
+```
+
 ### (Optional) Resource usage tuning

-Nextflow's labels can be used to specify the amount of resources a process can use. This workflow uses the following labels for CPU and memory:
-* `verylowmem`, `lowmem`, `midmem`, `highmem`
-* `verylowcpu`, `lowcpu`, `midcpu`, `highcpu`
+Nextflow’s labels can be used to specify the amount of resources a
+process can use. This workflow uses the following labels for CPU and
+memory:

-The defaults for these labels can be found at `src/config/labels.config`. Nextflow checks that the specified resources for a process do not exceed what is available on the machine and will not start if it does. Create your own config file to tune the labels to your needs, for example:
+- `verylowmem`, `lowmem`, `midmem`, `highmem`
+- `verylowcpu`, `lowcpu`, `midcpu`, `highcpu`

-```
-// Resource labels
-withLabel: verylowcpu { cpus = 2 }
-withLabel: lowcpu { cpus = 8 }
-withLabel: midcpu { cpus = 16 }
-withLabel: highcpu { cpus = 16 }
+The defaults for these labels can be found at
+`src/config/labels.config`. Nextflow checks that the specified resources
+for a process do not exceed what is available on the machine and will
+not start if it does. Create your own config file to tune the labels to
+your needs, for example:

-withLabel: verylowmem { memory = 4.GB }
-withLabel: lowmem { memory = 8.GB }
-withLabel: midmem { memory = 8.GB }
-withLabel: highmem { memory = 8.GB }
-```
+    // Resource labels
+    withLabel: verylowcpu { cpus = 2 }
+    withLabel: lowcpu { cpus = 8 }
+    withLabel: midcpu { cpus = 16 }
+    withLabel: highcpu { cpus = 16 }

-When starting nextflow using the CLI, you can use `-c` to provide the file to nextflow and overwrite the defaults.
+    withLabel: verylowmem { memory = 4.GB }
+    withLabel: lowmem { memory = 8.GB }
+    withLabel: midmem { memory = 8.GB }
+    withLabel: highmem { memory = 8.GB }

-### Example
-
-```bash
-nextflow run vsh/demultiplex \
-r v0.3.9 \
-main-script target/nextflow/runner/main.nf \
--input "gs://viash-hub-test-data/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2"  \
--demultiplexer bclconvert \
--publish_dir example_output/ \
-profile docker \
-c labels.config
-```
+When starting nextflow using the CLI, you can use `-c` to provide the
+file to nextflow and overwrite the defaults.

 ## Acknowledgements

 Developed in collaboration with Data Intuitive and Open Analytics.
-
-
--- a/README.qmd
+++ b/README.qmd
@@ -0,0 +1,191 @@
+---
+format: gfm
+---
+```{r setup, include=FALSE}
+project <- yaml::read_yaml("_viash.yaml")
+license <- paste0(project$links$repository, "/blob/main/LICENSE")
+```
+
+# Demultiplex.vsh
+
+Demultiplex.vsh is a workflow for demultiplexing of raw sequencing data. Currently data from Illumina and Element Biosciences sequencers are supported.
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-demultiplex-7a4baa.svg)](https://web.viash-hub.com/packages/demultiplex)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fdemultiplex-blue.svg)](https://github.com/viash-hub/demultiplex)
+[![GitHub
+License](https://img.shields.io/github/license/viash-hub/demultiplex.svg)](https://github.com/viash-hub/demultiplex/blob/main/LICENSE)
+[![GitHub
+Issues](https://img.shields.io/github/issues/viash-hub/demultiplex.svg)](https://github.com/viash-hub/demultiplex/issues)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.4-blue)](https://viash.io)
+
+## Introcuction
+This workflow is designed to demultiplex raw RNA-seq sequencing data from Illumina and Element Biosciences sequencers. 
+
+The workflow is built in a modular fashion, where most of the base functionality is provided by components from
+[`biobox`](https://www.viash-hub.com/packages/biobox/latest) supplemented by custom base components and workflow components in this package. Each of these components can be used independently as stand-alone modules with a 
+standardized interface.
+
+The full workflow can be run in two ways:
+
+1.  Run the [main
+    workflow](https://www.viash-hub.com/packages/demultiplex/v0.3.4/components/demultiplex)
+    containing the main functionality.
+2.  Run the [(opinianated)
+    `runner`](https://www.viash-hub.com/packages/demultiplex/v0.3.4/components/runner)
+    where a number of choices (input/output structure and location) have
+    been made.
+
+## Workflow Overview
+
+The workflow executes the following steps: 
+
+1. Unpacking the input data (when a TAR archive is provided)
+2. Run `bclconvert` or `bases2fastq` 
+3. Run `falco` and convert Illumina InterOp information to csv
+4. Run `multiqc` to generate a report
+
+## Example usage
+
+Two variants of the same workflow are provided, depending on the flexibility in the ouput structure required:
+
+* The `runner` workflow provides a predifined output structure. It requires the minimal amount of parameters to be provided, at the cost of being less flexible. It is located at `target/nextflow/runner/main.nf`
+* The `demultiplex` workflow (`target/nextflow/demultiplex/main.nf`) allows for more fine-grained tuning, but required more parameters to be provided.
+
+### Test data
+
+We have provided test data at `gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2` (Illumina), but please feel free to bring your own. The URL of the test data can be provided as-is to the workflow, or you can download everything and specify a local path.
+
+The input data should follow the structure of either Illumina or Element Biosciences sequencers. The workflow will automatically detect which demultiplexer to use (`bclconvert` or `bases2fastq`) based on the 
+presence of either `SampleSheet.csv` or `RunParameters.xml` in the input directory. Demultiplexer can also be set explicitly using the `--demultiplexer` parameter.
+
+### Setup
+
+In order to use the workflows in this package, you'll need to do the following:
+
+* Install [nextflow](https://www.nextflow.io/docs/latest/install.html)
+* Install a nextflow compatible executor. This workflow provides a profile for [docker](https://docs.docker.com/get-started/).
+
+### Run from Viash Hub
+
+1. Open [Viash Hub](https://www.viash-hub.com) and browse to the [demultiplex
+component](https://www.viash-hub.com/packages/demultiplex/v0.3.4/components/demultiplex).
+Press the ‘Launch’ button and follow the instructions.
+
+![](assets/demultiplex-launch-small.png)
+
+2. We will start an example run and set profile to `docker`.
+
+![](assets/demultiplex-launch-parameters-1.png)
+
+3. In the next step, we provide the paramters as follows and leave the rest as defalut:
+
+- `input`:
+  `gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2`
+
+![](assets/demultiplex-launch-parameters-2.png)
+
+Press the ‘Launch’ button at the end to get the instructions on how to
+run the workflow from the CLI.
+
+### Run using NF-Tower / Seqera Cloud
+
+It’s possible to run the workflow directly from [Seqera
+Cloud](https://cloud.seqera.io). The necessary [Nextflow schema
+file](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/)
+has been built and provided with the workflows in order to use the
+form-based input.
+
+1. Select the option to run the workflow using Seqera Cloud. You
+will need to create an API token for your account. Once this token is
+filled in in the corresponding field, we will get the option to select
+a ‘Workspace’ and a ‘Compute environment’.
+
+![](assets/demultiplex-launch-parameters-3.png)
+
+2. Provide the parameters similar to the previous step.
+
+3. In the next screen, pressing the ‘Launch’ button will actually start the
+workflow on Seqera Cloud. A message is shown when the submit was
+successful.
+
+![](assets/demultiplex-launch-parameters-4.png)
+
+### Setting up SCM
+
+In order to let nextflow use the viash-hub workflows, you need to setup a [SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) file. This can be done once by creating `$HOME/.nextflow/scm` and adding the following:
+```
+providers {
+   vsh {
+    platform = 'gitlab'
+    server = "packages.viash-hub.com"
+  }
+}
+```
+
+Alternatively, a custom location for the SCM file can be specified using the `NXF_SCM_FILE` environment variable.
+
+You can check if everything is working by getting the `--help` for a workflow:
+```bash
+nextflow run \
+vsh/demultiplex \
+-r v0.3.11 \
+--help
+```
+
+### Run from the CLI
+
+Running from the CLI directly without using Viash hub is possible as well. The
+easiest is to use the integrated help functionality, for instance
+using the following:
+
+``` bash
+ nextflow run vsh/demultiplex \
+  -revision v0.3.11 \
+  -main-script target/nextflow/workflows/runner/main.nf \
+  --help
+```
+
+Having this project available locally, you can run the following command:
+
+```bash
+nextflow run vsh/demultiplex \
+-r v0.3.11 \
+-main-script target/nextflow/runner/main.nf \
+--input "gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2"  \
+--demultiplexer bclconvert \
+--skip_copycomplete_check \
+--publish_dir example_output/ \
+-profile docker \
+-c src/config/labels.config
+```
+
+### (Optional) Resource usage tuning
+
+Nextflow's labels can be used to specify the amount of resources a process can use. This workflow uses the following labels for CPU and memory:
+
+* `verylowmem`, `lowmem`, `midmem`, `highmem`
+* `verylowcpu`, `lowcpu`, `midcpu`, `highcpu`
+
+The defaults for these labels can be found at `src/config/labels.config`. Nextflow checks that the specified resources for a process do not exceed what is available on the machine and will not start if it does. Create your own config file to tune the labels to your needs, for example:
+
+```
+// Resource labels
+withLabel: verylowcpu { cpus = 2 }
+withLabel: lowcpu { cpus = 8 }
+withLabel: midcpu { cpus = 16 }
+withLabel: highcpu { cpus = 16 }
+
+withLabel: verylowmem { memory = 4.GB }
+withLabel: lowmem { memory = 8.GB }
+withLabel: midmem { memory = 8.GB }
+withLabel: highmem { memory = 8.GB }
+```
+
+When starting nextflow using the CLI, you can use `-c` to provide the file to nextflow and overwrite the defaults.
+
+## Acknowledgements
+
+Developed in collaboration with Data Intuitive and Open Analytics.
+
+
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.9
+version: v0.3.11
 description: |
  Demultiplexing pipeline
 license: MIT
@@ -9,7 +9,7 @@ links:
  repository: https://github.com/viash-hub/demultiplex
 info:
  test_resources:
-    - path: gs://viash-hub-test-data/demultiplex/v2/
+    - path: gs://viash-hub-resources/demultiplex/v3
      dest: testData

 viash_version: 0.9.4
--- a/assets/demultiplex-launch-parameters-1.png
+++ b/assets/demultiplex-launch-parameters-1.png
--- a/assets/demultiplex-launch-parameters-2.png
+++ b/assets/demultiplex-launch-parameters-2.png
--- a/assets/demultiplex-launch-parameters-3.png
+++ b/assets/demultiplex-launch-parameters-3.png
--- a/assets/demultiplex-launch-parameters-4.png
+++ b/assets/demultiplex-launch-parameters-4.png
--- a/assets/demultiplex-launch-small.png
+++ b/assets/demultiplex-launch-small.png
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -54,6 +54,11 @@ argument_groups:
        direction: "output"
        required: true
        default: "$id/run_information.csv"
+      - name: "--demultiplexer_logs"
+        type: file
+        direction: output
+        required: true
+        default: "$id/demultiplexer_logs"
  - name: "Other arguments"
    arguments:
      - name: --skip_copycomplete_check
--- a/src/demultiplex/main.nf
+++ b/src/demultiplex/main.nf
@@ -124,14 +124,15 @@ workflow run_wf {
            bcl_input_directory: state.input,
            sample_sheet: state.run_information,
            output_directory: state.output,
-            reports: "reports",
-            logs: "logs"
+            reports: state.demultiplexer_logs,
+            logs: state.demultiplexer_logs,
          ]
        },
        toState: {id, result, state -> 
          def toAdd = [
            "output_demultiplexer" : result.output_directory,
            "run_id": id,
+            "demultiplexer_logs": result.reports,
          ]
          def newState = state + toAdd
          return newState
@@ -141,11 +142,15 @@ workflow run_wf {
      | bases2fastq.run(
        runIf: {id, state -> state.demultiplexer in ["bases2fastq"]},
        directives: [label: ["highmem", "midcpu"]],
-        fromState: [
-          "analysis_directory": "input",
-          "run_manifest": "run_information",
-          "output_directory": "output",
-        ],
+        fromState: { id, state ->
+          [
+            "analysis_directory": state.input,
+            "run_manifest": state.run_information,
+            "output_directory": state.output,
+            "report": state.demultiplexer_logs + "/report.html",
+            "logs": state.demultiplexer_logs,
+          ]
+        },
        args: [
          "no_projects": true, // Do not put output files in a subfolder for project
          //"split_lanes": true,
@@ -156,6 +161,8 @@ workflow run_wf {
          def toAdd = [
            "output_demultiplexer" : result.output_directory,
            "run_id": id,
+            "demultiplexer_logs": result.logs,
+
          ]
          def newState = state + toAdd
          return newState
@@ -225,6 +232,7 @@ workflow run_wf {
          state + [ "output_multiqc" : result.output_report ]
        }
      )
+
      | setState(
        [
          //"_meta": "_meta",
@@ -232,6 +240,7 @@ workflow run_wf {
          "output_falco": "output_falco",
          "output_multiqc": "output_multiqc",
          "output_run_information": "run_information",
+          "demultiplexer_logs": "demultiplexer_logs"
        ]
      )

--- a/src/demultiplex/test.nf
+++ b/src/demultiplex/test.nf
@@ -23,6 +23,14 @@ workflow test_illumina {
        assert output.size() == 2 : "outputs should contain two elements; [id, file]"
        "Output: $output"
      }
+
+  event_count_ch = output_ch
+    | toSortedList()
+    | map { state -> 
+      assert state.size() == 1 : "Expected one event in the output channel"
+    }
+
+  assert_ch = output_ch
    | map {id, state ->
      assert state.output.isDirectory(): "Expected bclconvert output to be a directory"
      state.output_falco.each{
@@ -57,6 +65,21 @@ workflow test_illumina {
                                   |1,sampletest,PatientSample,UDP0004,ATTCCATAAG,TGCCTGGTGG
                                   |""".stripMargin()
      assert state.output_run_information.text.replaceAll("\r\n", "\n") == expected_run_information
+
+      println "ID: ${id}"
+      println "State: ${state}"
+
+      assert state.demultiplexer_logs.isDirectory(): 
+        "Expected BCL Convert reports to be a directory"
+        
+      def logs_files = state.demultiplexer_logs.listFiles()
+      println "Logs files: ${logs_files}"
+      assert logs_files.size() > 0: "Expected BCL Convert logs dir to contain files"
+      
+      assert logs_files.find { it.name == "Demultiplex_Stats.csv" }: 
+        "Expected to find BCL Convert Demultiplex_Stats.csv"
+      assert logs_files.find { it.name == "Logs" }: 
+        "Expected to find BCL Convert Logs directory"
    }
 }

@@ -80,5 +103,14 @@ workflow test_bases2fastq {
      assert state.output.isDirectory(): "Expected bases2fastq output to be a directory"
      state.output_falco.each{assert it.isDirectory(): "Expected falco output to be a directory"}
      assert state.output_multiqc.isFile(): "Expected multiQC output to be a file"
+
+      def logs_files = state.demultiplexer_logs.listFiles()
+      println "Logs files: ${logs_files}"
+      assert logs_files.size() > 0: "Expected bases2fastq logs dir to contain files"
+
+      assert logs_files.find { it.name == "report.html" } != null: 
+        "Expected to find bases2fastq report.html"
+      assert logs_files.find { it.name == "info" }: 
+        "Expected to find bases2fastq info directory"
    }
 }
--- a/src/io/interop_summary_to_csv/config.vsh.yaml
+++ b/src/io/interop_summary_to_csv/config.vsh.yaml
@@ -22,6 +22,10 @@ requirements:
 resources:
  - type: bash_script
    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: /testData/iseq-DI
 engines:
  - type: docker
    image: debian:stable-slim
--- a/src/io/interop_summary_to_csv/test.sh
+++ b/src/io/interop_summary_to_csv/test.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+# create tempdir
+echo ">>> Creating temporary test directory."
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+echo ">>> Created temporary directory '$TMPDIR'."
+
+echo ">>> Run simple execution"
+./$meta_functionality_name \
+   --input "$meta_resources_dir/iseq-DI" \
+   --output_run_summary "$TMPDIR/run_summary.csv" \
+   --output_index_summary "$TMPDIR/index_summary.csv"
--- a/src/io/publish/code.sh
+++ b/src/io/publish/code.sh
@@ -5,6 +5,7 @@ set -eo pipefail
 declare -A input_output_mapping=(["par_input"]="par_output" 
                                 ["par_input_multiqc"]="par_output_multiqc"
                                 ["par_input_run_information"]="par_output_run_information"
+                                 ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs"
                                )

 for input_argument_name in "${!input_output_mapping[@]}"
--- a/src/io/publish/config.vsh.yaml
+++ b/src/io/publish/config.vsh.yaml
@@ -21,6 +21,9 @@ argument_groups:
        description: "Location where to write the run information to."
        type: file
        required: true
+      - name: "--input_demultiplexer_logs"
+        type: file
+        required: true
  - name: Output arguments
    arguments:
      - name: --output
@@ -39,6 +42,10 @@ argument_groups:
        type: file
        direction: output
        default: run_information.csv
+      - name: "--output_demultiplexer_logs"
+        type: file
+        direction: output
+        default: "demultiplexer_logs"

 resources:
  - type: bash_script
--- a/src/runner/config.vsh.yaml
+++ b/src/runner/config.vsh.yaml
@@ -49,6 +49,10 @@ argument_groups:
        type: file
        direction: output
        default: "qc/multiqc_report.html"
+      - name: "--demultiplexer_logs"
+        type: file
+        direction: output
+        default: "demultiplexer_logs"
  - name: "Other arguments"
    arguments:
      - name: --skip_copycomplete_check
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -28,6 +28,7 @@ workflow run_wf {
            "output": "$id/fastq",
            "output_falco": "$id/qc/fastqc",
            "output_multiqc": "$id/qc/multiqc_report.html",
+            "demultiplexer_logs": "$id/demultiplexer_logs",
          ]
          if (state.run_information) {
            state_to_pass += ["output_run_information": state.run_information.getName()] 
@@ -48,6 +49,7 @@ workflow run_wf {
          def falco_output_1 = (id2 == "run") ? state.falco_output : "${id2}/" + state.falco_output
          def multiqc_output_1 = (id2 == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
          def run_information_output_1 = (id2 == "run") ? "${state.output_run_information.getName()}" : "${id2}/${state.output_run_information.getName()}"
+          def demultiplexer_logs_output = (id2 == "run") ? state.demultiplexer_logs : "${id2}/${state.demultiplexer_logs.getName()}"

          if (id2 == "run") {
            println("Publising to ${params.publish_dir}")
@@ -60,10 +62,12 @@ workflow run_wf {
            input_falco: state.output_falco,
            input_multiqc: state.output_multiqc,
            input_run_information: state.output_run_information,
+            input_demultiplexer_logs: state.demultiplexer_logs,
            output: fastq_output_1,
            output_falco: falco_output_1,
            output_multiqc: multiqc_output_1,
            output_run_information: run_information_output_1,
+            output_demultiplexer_logs: demultiplexer_logs_output,
          ]
        },
        toState: { id, result, state -> [:] },
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -41,6 +41,12 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "iseq-DI"
 info: null
 status: "enabled"
 scope:
@@ -126,7 +132,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.9"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -151,16 +157,16 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -172,7 +178,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# interop_summary_to_csv v0.3.9
+# interop_summary_to_csv v0.3.11
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2025-04-25T12:13:39Z"
+LABEL org.opencontainers.image.created="2025-05-14T08:46:02Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="820318c378d8119e2aa98768282e43c2aa017ba7"
-LABEL org.opencontainers.image.version="v0.3.9"
+LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
+LABEL org.opencontainers.image.version="v0.3.11"

 VIASHDOCKER
  fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.3.9"
+  echo "interop_summary_to_csv v0.3.11"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.3.9"
+            echo "interop_summary_to_csv v0.3.11"
            exit
            ;;
        --input)
@@ -759,7 +759,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.9'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.11'
  fi

  # print dockerfile
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -44,6 +44,15 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--input_demultiplexer_logs"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output arguments"
  arguments:
  - type: "file"
@@ -90,6 +99,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--output_demultiplexer_logs"
+    info: null
+    default:
+    - "demultiplexer_logs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
  path: "code.sh"
@@ -181,7 +201,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.9"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -199,16 +219,16 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -220,7 +240,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish v0.3.9
+# publish v0.3.11
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2025-04-25T12:13:38Z"
+LABEL org.opencontainers.image.created="2025-05-14T08:46:03Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="820318c378d8119e2aa98768282e43c2aa017ba7"
-LABEL org.opencontainers.image.version="v0.3.9"
+LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
+LABEL org.opencontainers.image.version="v0.3.11"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.3.9"
+  echo "publish v0.3.11"
  echo ""
  echo "Publish the processed results of the run"
  echo ""
@@ -591,6 +591,9 @@ function ViashHelp {
  echo "        type: file, required parameter, file must exist"
  echo "        Location where to write the run information to."
  echo ""
+  echo "    --input_demultiplexer_logs"
+  echo "        type: file, required parameter, file must exist"
+  echo ""
  echo "Output arguments:"
  echo "    --output"
  echo "        type: file, output, file must exist"
@@ -608,6 +611,10 @@ function ViashHelp {
  echo "        type: file, output, file must exist"
  echo "        default: run_information.csv"
  echo ""
+  echo "    --output_demultiplexer_logs"
+  echo "        type: file, output, file must exist"
+  echo "        default: demultiplexer_logs"
+  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
@@ -655,7 +662,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish v0.3.9"
+            echo "publish v0.3.11"
            exit
            ;;
        --input)
@@ -708,6 +715,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --input_demultiplexer_logs)
+            [ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --input_demultiplexer_logs=*)
+            [ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs=*\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(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"
@@ -752,6 +770,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --output_demultiplexer_logs)
+            [ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --output_demultiplexer_logs=*)
+            [ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs=*\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
@@ -840,7 +869,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.9'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.11'
  fi

  # print dockerfile
@@ -940,6 +969,10 @@ if [ -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then
  ViashError '--input_run_information' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
 fi
+if [ -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then
+  ViashError '--input_demultiplexer_logs' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
 if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
@@ -978,6 +1011,9 @@ fi
 if [ -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then
  VIASH_PAR_OUTPUT_RUN_INFORMATION="run_information.csv"
 fi
+if [ -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then
+  VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="demultiplexer_logs"
+fi

 # check whether required files exist
 if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -1004,6 +1040,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_INPUT_RUN_I
  ViashError "Input file '$VIASH_PAR_INPUT_RUN_INFORMATION' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
+  ViashError "Input file '$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS' does not exist."
+  exit 1
+fi

 # check whether parameters values are of the right type
 if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -1092,6 +1132,9 @@ fi
 if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")"
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")"
+fi

 if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  if [ "$VIASH_MODE" == "run" ]; then
@@ -1128,6 +1171,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_RUN_INFORMATION")" )
  VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_RUN_INFORMATION")
 fi
+if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")" )
+  VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")
+fi
 if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
@@ -1148,6 +1195,11 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
  VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_RUN_INFORMATION" )
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" )
+  VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" )
+fi
 if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1221,10 +1273,12 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'
 $( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi )
 $( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi )
 $( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi )
+$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; 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 ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; 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 )
@@ -1252,6 +1306,7 @@ set -eo pipefail
 declare -A input_output_mapping=(["par_input"]="par_output" 
                                 ["par_input_multiqc"]="par_output_multiqc"
                                 ["par_input_run_information"]="par_output_run_information"
+                                 ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs"
                                )

 for input_argument_name in "\${!input_output_mapping[@]}"
@@ -1310,6 +1365,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
    VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_RUN_INFORMATION")
  fi
+  if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
+    VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")
+  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
@@ -1322,6 +1380,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
    VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
  fi
+  if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
+    VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")
+  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
@@ -1354,6 +1415,10 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_OUTPUT_RUN
  ViashError "Output file '$VIASH_PAR_OUTPUT_RUN_INFORMATION' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
+  ViashError "Output file '$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS' does not exist."
+  exit 1
+fi


 exit 0
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -138,7 +138,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.9"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -156,16 +156,16 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -177,7 +177,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# untar v0.3.9
+# untar v0.3.11
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2025-04-25T12:13:38Z"
+LABEL org.opencontainers.image.created="2025-05-14T08:46:02Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="820318c378d8119e2aa98768282e43c2aa017ba7"
-LABEL org.opencontainers.image.version="v0.3.9"
+LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
+LABEL org.opencontainers.image.version="v0.3.11"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.9"
+  echo "untar v0.3.11"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.9"
+            echo "untar v0.3.11"
            exit
            ;;
        --input)
@@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.9'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.11'
  fi

  # print dockerfile
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -165,16 +165,16 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -186,7 +186,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.3.9
+// combine_samples v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3230,18 +3230,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3253,7 +3253,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/combine_samples'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }

--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -141,16 +141,16 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -162,7 +162,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.9
+// gather_fastqs_and_validate v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3203,18 +3203,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3226,7 +3226,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/gather_fastqs_and_validate'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }

--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -96,6 +96,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--demultiplexer_logs"
+    info: null
+    default:
+    - "$id/demultiplexer_logs"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 - name: "Other arguments"
  arguments:
  - type: "boolean_true"
@@ -247,9 +258,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -261,11 +272,11 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -277,7 +288,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.3.9
+// demultiplex v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "demultiplex",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3139,6 +3139,19 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--demultiplexer_logs",
+          "default" : [
+            "$id/demultiplexer_logs"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -3350,18 +3363,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3373,7 +3386,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3530,14 +3543,15 @@ workflow run_wf {
            bcl_input_directory: state.input,
            sample_sheet: state.run_information,
            output_directory: state.output,
-            reports: "reports",
-            logs: "logs"
+            reports: state.demultiplexer_logs,
+            logs: state.demultiplexer_logs,
          ]
        },
        toState: {id, result, state -> 
          def toAdd = [
            "output_demultiplexer" : result.output_directory,
            "run_id": id,
+            "demultiplexer_logs": result.reports,
          ]
          def newState = state + toAdd
          return newState
@@ -3547,11 +3561,15 @@ workflow run_wf {
      | bases2fastq.run(
        runIf: {id, state -> state.demultiplexer in ["bases2fastq"]},
        directives: [label: ["highmem", "midcpu"]],
-        fromState: [
-          "analysis_directory": "input",
-          "run_manifest": "run_information",
-          "output_directory": "output",
-        ],
+        fromState: { id, state ->
+          [
+            "analysis_directory": state.input,
+            "run_manifest": state.run_information,
+            "output_directory": state.output,
+            "report": state.demultiplexer_logs + "/report.html",
+            "logs": state.demultiplexer_logs,
+          ]
+        },
        args: [
          "no_projects": true, // Do not put output files in a subfolder for project
          //"split_lanes": true,
@@ -3562,6 +3580,8 @@ workflow run_wf {
          def toAdd = [
            "output_demultiplexer" : result.output_directory,
            "run_id": id,
+            "demultiplexer_logs": result.logs,
+
          ]
          def newState = state + toAdd
          return newState
@@ -3631,6 +3651,7 @@ workflow run_wf {
          state + [ "output_multiqc" : result.output_report ]
        }
      )
+
      | setState(
        [
          //"_meta": "_meta",
@@ -3638,6 +3659,7 @@ workflow run_wf {
          "output_falco": "output_falco",
          "output_multiqc": "output_multiqc",
          "output_run_information": "run_information",
+          "demultiplexer_logs": "demultiplexer_logs"
        ]
      )

--- a/target/nextflow/demultiplex/nextflow.config
+++ b/target/nextflow/demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'demultiplex'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
  description = 'Demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/demultiplex/nextflow_schema.json
+++ b/target/nextflow/demultiplex/nextflow_schema.json
@@ -109,6 +109,17 @@
            }
    

+        ,
+                "demultiplexer_logs": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id/demultiplexer_logs`. ",
+                "help_text": "Type: `file`, required, default: `$id/demultiplexer_logs`. "
+            ,
+                "default":"$id/demultiplexer_logs"
+            }
+    
+
 }
 },
    
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -41,6 +41,12 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "iseq-DI"
 info: null
 status: "enabled"
 scope:
@@ -126,7 +132,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.9"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -151,16 +157,16 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -172,7 +178,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.3.9
+// interop_summary_to_csv v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "interop_summary_to_csv",
  "namespace" : "io",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3088,6 +3088,17 @@ meta = [
      "dest" : "nextflow_labels.config"
    }
  ],
+  "test_resources" : [
+    {
+      "type" : "bash_script",
+      "path" : "test.sh",
+      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/testData/iseq-DI"
+    }
+  ],
  "status" : "enabled",
  "scope" : {
    "image" : "public",
@@ -3187,7 +3198,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.9",
+      "target_tag" : "v0.3.11",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3217,18 +3228,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3240,7 +3251,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3684,7 +3695,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.9"
+    "tag" : "v0.3.11"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/interop_summary_to_csv/nextflow.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/interop_summary_to_csv'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -44,6 +44,15 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--input_demultiplexer_logs"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output arguments"
  arguments:
  - type: "file"
@@ -90,6 +99,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--output_demultiplexer_logs"
+    info: null
+    default:
+    - "demultiplexer_logs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
  path: "code.sh"
@@ -181,7 +201,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.9"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -199,16 +219,16 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -220,7 +240,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.3.9
+// publish v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish",
  "namespace" : "io",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3080,6 +3080,16 @@ meta = [
          "direction" : "input",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--input_demultiplexer_logs",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -3137,6 +3147,19 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--output_demultiplexer_logs",
+          "default" : [
+            "demultiplexer_logs"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    }
@@ -3251,7 +3274,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.9",
+      "target_tag" : "v0.3.11",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3274,18 +3297,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3297,7 +3320,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3330,10 +3353,12 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'
 $( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi )
 $( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi )
 $( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi )
+$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; 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 ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; 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 )
@@ -3361,6 +3386,7 @@ set -eo pipefail
 declare -A input_output_mapping=(["par_input"]="par_output" 
                                 ["par_input_multiqc"]="par_output_multiqc"
                                 ["par_input_run_information"]="par_output_run_information"
+                                 ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs"
                                )

 for input_argument_name in "\\${!input_output_mapping[@]}"
@@ -3769,7 +3795,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.9"
+    "tag" : "v0.3.11"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish/nextflow.config
+++ b/target/nextflow/io/publish/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
  description = 'Publish the processed results of the run'
 }

--- a/target/nextflow/io/publish/nextflow_schema.json
+++ b/target/nextflow/io/publish/nextflow_schema.json
@@ -53,6 +53,16 @@
            }
    

+        ,
+                "input_demultiplexer_logs": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. ",
+                "help_text": "Type: `file`, required. "
+            
+            }
+    
+
 }
 },
    
@@ -107,6 +117,17 @@
            }
    

+        ,
+                "output_demultiplexer_logs": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `demultiplexer_logs`. ",
+                "help_text": "Type: `file`, default: `demultiplexer_logs`. "
+            ,
+                "default":"demultiplexer_logs"
+            }
+    
+
 }
 },
    
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -138,7 +138,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.9"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -156,16 +156,16 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -177,7 +177,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.3.9
+// untar v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
  "namespace" : "io",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3204,7 +3204,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.9",
+      "target_tag" : "v0.3.11",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3227,18 +3227,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3250,7 +3250,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3724,7 +3724,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.9"
+    "tag" : "v0.3.11"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/untar/nextflow.config
+++ b/target/nextflow/io/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/untar'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
  description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }

--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.3.9"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -84,6 +84,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--demultiplexer_logs"
+    info: null
+    default:
+    - "demultiplexer_logs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 - name: "Other arguments"
  arguments:
  - type: "boolean_true"
@@ -195,19 +206,19 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.4"
-  git_commit: "820318c378d8119e2aa98768282e43c2aa017ba7"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.8-5-g820318c"
+  git_tag: "v0.3.10-5-gcd2cfac"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.3.9"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
-    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
@@ -219,7 +230,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.3.9
+// runner v0.3.11
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "runner",
-  "version" : "v0.3.9",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3125,6 +3125,19 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--demultiplexer_logs",
+          "default" : [
+            "demultiplexer_logs"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -3270,18 +3283,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "820318c378d8119e2aa98768282e43c2aa017ba7",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.8-5-g820318c"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.9",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
        {
-          "path" : "gs://viash-hub-test-data/demultiplex/v2/",
+          "path" : "gs://viash-hub-resources/demultiplex/v3",
          "dest" : "testData"
        }
      ]
@@ -3293,7 +3306,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.9'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3348,6 +3361,7 @@ workflow run_wf {
            "output": "$id/fastq",
            "output_falco": "$id/qc/fastqc",
            "output_multiqc": "$id/qc/multiqc_report.html",
+            "demultiplexer_logs": "$id/demultiplexer_logs",
          ]
          if (state.run_information) {
            state_to_pass += ["output_run_information": state.run_information.getName()] 
@@ -3368,6 +3382,7 @@ workflow run_wf {
          def falco_output_1 = (id2 == "run") ? state.falco_output : "${id2}/" + state.falco_output
          def multiqc_output_1 = (id2 == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
          def run_information_output_1 = (id2 == "run") ? "${state.output_run_information.getName()}" : "${id2}/${state.output_run_information.getName()}"
+          def demultiplexer_logs_output = (id2 == "run") ? state.demultiplexer_logs : "${id2}/${state.demultiplexer_logs.getName()}"

          if (id2 == "run") {
            println("Publising to ${params.publish_dir}")
@@ -3380,10 +3395,12 @@ workflow run_wf {
            input_falco: state.output_falco,
            input_multiqc: state.output_multiqc,
            input_run_information: state.output_run_information,
+            input_demultiplexer_logs: state.demultiplexer_logs,
            output: fastq_output_1,
            output_falco: falco_output_1,
            output_multiqc: multiqc_output_1,
            output_run_information: run_information_output_1,
+            output_demultiplexer_logs: demultiplexer_logs_output,
          ]
        },
        toState: { id, result, state -> [:] },
--- a/target/nextflow/runner/nextflow.config
+++ b/target/nextflow/runner/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'runner'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.9'
+  version = 'v0.3.11'
  description = 'Runner for demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/runner/nextflow_schema.json
+++ b/target/nextflow/runner/nextflow_schema.json
@@ -109,6 +109,17 @@
            }
    

+        ,
+                "demultiplexer_logs": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `demultiplexer_logs`. ",
+                "help_text": "Type: `file`, default: `demultiplexer_logs`. "
+            ,
+                "default":"demultiplexer_logs"
+            }
+    
+
 }
 },