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
2025-05-14 09:11:58 +00:00
43 changed files with 501 additions and 153 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# demultiplex v0.3.11
+
+# New features
+
+* Output demultiplexer logs and metrics (PR #41).
+
 # demultiplex v0.3.10

 ## Minor changes
--- a/README.md
+++ b/README.md
@@ -153,7 +153,7 @@ workflow:
 ``` bash
 nextflow run \
 vsh/demultiplex \
-r v0.3.9 \
+-r v0.3.11 \
 --help
 ```

@@ -165,7 +165,7 @@ instance using the following:

 ``` bash
 nextflow run vsh/demultiplex \
-  -revision v0.3.9 \
+  -revision v0.3.11 \
  -main-script target/nextflow/workflows/runner/main.nf \
  --help
 ```
@@ -175,7 +175,7 @@ command:

 ``` bash
 nextflow run vsh/demultiplex \
-r v0.3.9 \
+-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 \
--- a/README.qmd
+++ b/README.qmd
@@ -129,7 +129,7 @@ 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
 ```

@@ -141,7 +141,7 @@ using the following:

 ``` bash
 nextflow run vsh/demultiplex \
-  -revision v0.3.9 \
+  -revision v0.3.11 \
  -main-script target/nextflow/workflows/runner/main.nf \
  --help
 ```
@@ -150,7 +150,7 @@ Having this project available locally, you can run the following command:

 ```bash
 nextflow run vsh/demultiplex \
-r v0.3.9 \
+-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 \
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.10
+version: v0.3.11
 description: |
  Demultiplexing pipeline
 license: MIT
--- 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: "v0.3.10"
+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: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -151,12 +157,12 @@ 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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -172,7 +178,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+# 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="2025-05-07T11:20:11Z"
+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="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
-LABEL org.opencontainers.image.version="v0.3.10"
+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 v0.3.10"
+  echo "interop_summary_to_csv v0.3.11"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.3.10"
+            echo "interop_summary_to_csv v0.3.11"
            exit
            ;;
        --input)
@@ -759,7 +759,7 @@ if [[ "$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:v0.3.10'
+    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: "v0.3.10"
+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: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -199,12 +219,12 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -220,7 +240,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+# 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="2025-05-07T11:20:10Z"
+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="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
-LABEL org.opencontainers.image.version="v0.3.10"
+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 v0.3.10"
+  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 v0.3.10"
+            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:v0.3.10'
+    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: "v0.3.10"
+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: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -156,12 +156,12 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -177,7 +177,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+# 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="2025-05-07T11:20:10Z"
+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="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
-LABEL org.opencontainers.image.version="v0.3.10"
+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 v0.3.10"
+  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 [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.10"
+            echo "untar v0.3.11"
            exit
            ;;
        --input)
@@ -771,7 +771,7 @@ if [[ "$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:v0.3.10'
+    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: "v0.3.10"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -165,12 +165,12 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -186,7 +186,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3230,13 +3230,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -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 := 'v0.3.10'"
+      ".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 = 'v0.3.10'
+  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: "v0.3.10"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -141,12 +141,12 @@ 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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -162,7 +162,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "version" : "v0.3.11",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3203,13 +3203,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -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 := 'v0.3.10'"
+      ".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 = 'v0.3.10'
+  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: "v0.3.10"
+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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -261,7 +272,7 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -277,7 +288,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "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" : ";"
        }
      ]
    },
@@ -3350,13 +3363,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -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 := 'v0.3.10'"
+      ".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 = 'v0.3.10'
+  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: "v0.3.10"
+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: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -151,12 +157,12 @@ 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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -172,7 +178,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "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" : "v0.3.10",
+      "target_tag" : "v0.3.11",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3217,13 +3228,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3240,7 +3251,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3684,7 +3695,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.10"
+    "tag" : "v0.3.11"
  },
  "tag" : "$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 = 'v0.3.10'
+  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: "v0.3.10"
+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: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -199,12 +219,12 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -220,7 +240,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "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" : "v0.3.10",
+      "target_tag" : "v0.3.11",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3274,13 +3297,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -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 := 'v0.3.10'"
+      ".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" : "v0.3.10"
+    "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 = 'v0.3.10'
+  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: "v0.3.10"
+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: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -156,12 +156,12 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -177,7 +177,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "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" : "v0.3.10",
+      "target_tag" : "v0.3.11",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3227,13 +3227,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3250,7 +3250,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3724,7 +3724,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.10"
+    "tag" : "v0.3.11"
  },
  "tag" : "$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 = 'v0.3.10'
+  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: "v0.3.10"
+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"
@@ -195,15 +206,15 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -219,7 +230,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".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 v0.3.10
+// 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" : "v0.3.10",
+  "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" : ";"
        }
      ]
    },
@@ -3270,13 +3283,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6",
+    "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.10"
+    "git_tag" : "v0.3.10-5-gcd2cfac"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.10",
+    "version" : "v0.3.11",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3293,7 +3306,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3348,6 +3361,7 @@ workflow run_wf {
            "output": "$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 = 'v0.3.10'
+  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"
+            }
+    
+
 }
 },