Build branch v0.3 with version v0.3.3 (e297e8f)

Build pipeline: viash-hub.demultiplex.v0.3-dd5mz Source commit: e297e8ff45 Source message: Bump version to v0.3.3
Build branch v0.3 with version v0.3.2 (7ad45f3)
2024-12-19 15:56:52 +00:00 · 2024-12-11 18:07:49 +00:00
40 changed files with 598 additions and 303 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,64 @@
+# demultiplex v0.3.3
+
+## Breaking change
+
+- The `runner` defines the output differently now:
+
+  - The last part of the `--input` path is expected to be the run ID and this run ID is used to create the output directory.
+  - If the input is `file.tar.gz` instead of a directory, the `file` part is used as the run ID.
+
+- The output structure is then as follows:
+
+    ```
+    $publish_dir/<run_id>/<date_time_stamp>_demultiplex_<version>/
+    ```
+
+    For instance:
+
+    ```
+    $publish_dir
+    └── 200624_A00834_0183_BHMTFYDRXX
+        └── 20241217_051404_demultiplex_v1.2
+            ├── run_information.csv
+            ├── fastq
+            │   ├── Sample1_S1_L001_R1_001.fastq.gz
+            │   ├── Sample23_S3_L001_R1_001.fastq.gz
+            │   ├── SampleA_S2_L001_R1_001.fastq.gz
+            │   ├── Undetermined_S0_L001_R1_001.fastq.gz
+            │   └── sampletest_S4_L001_R1_001.fastq.gz
+            └── qc
+                ├── fastqc
+                │   ├── Sample1_S1_L001_R1_001.fastq.gz_fastqc_data.txt
+                │   ├── Sample1_S1_L001_R1_001.fastq.gz_fastqc_report.html
+                │   ├── Sample1_S1_L001_R1_001.fastq.gz_summary.txt
+                │   ├── Sample23_S3_L001_R1_001.fastq.gz_fastqc_data.txt
+                │   ├── Sample23_S3_L001_R1_001.fastq.gz_fastqc_report.html
+                │   ├── Sample23_S3_L001_R1_001.fastq.gz_summary.txt
+                │   ├── SampleA_S2_L001_R1_001.fastq.gz_fastqc_data.txt
+                │   ├── SampleA_S2_L001_R1_001.fastq.gz_fastqc_report.html
+                │   ├── SampleA_S2_L001_R1_001.fastq.gz_summary.txt
+                │   ├── Undetermined_S0_L001_R1_001.fastq.gz_fastqc_data.txt
+                │   ├── Undetermined_S0_L001_R1_001.fastq.gz_fastqc_report.html
+                │   ├── Undetermined_S0_L001_R1_001.fastq.gz_summary.txt
+                │   ├── sampletest_S4_L001_R1_001.fastq.gz_fastqc_data.txt
+                │   ├── sampletest_S4_L001_R1_001.fastq.gz_fastqc_report.html
+                │   └── sampletest_S4_L001_R1_001.fastq.gz_summary.txt
+                └── multiqc_report.html
+
+    ```
+
+- This logic can be avoided by providing the flag `--plain_output`.
+
+# Minor updates
+
+* Added `output_run_information` argument that copies the run information file to the output (PR #31).
+
+# demultiplex v0.3.2
+
+# Bug fixes
+
+* Ignore empty CSV entries when parsing sample information (PR #29).
+
 # demultiplex v0.3.1

 # Minor updates
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.1
+version: v0.3.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/src/dataflow/gather_fastqs_and_validate/main.nf
+++ b/src/dataflow/gather_fastqs_and_validate/main.nf
@@ -50,7 +50,10 @@ workflow run_wf {
              println "Found sample names column '${csv_items[sample_id_column_index]}'."
              return
            }
-            samples += csv_items[sample_id_column_index]
+            def candidate_sample_id = csv_items[sample_id_column_index]
+            if (candidate_sample_id?.trim()) { // Don't add empty csv entries.
+              samples += csv_items[sample_id_column_index]
+            }
          }
          // This return is important! (If 'true' is returned, the parsing stops.)
          return 
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -48,6 +48,11 @@ argument_groups:
        direction: output
        required: false
        default: "$id/qc/multiqc_report.html"
+      - name: "--output_run_information"
+        type: file
+        direction: "output"
+        required: true
+        default: "$id/run_information.csv"
 resources:
  - type: nextflow_script
    path: main.nf
--- a/src/demultiplex/main.nf
+++ b/src/demultiplex/main.nf
@@ -225,7 +225,8 @@ workflow run_wf {
          //"_meta": "_meta",
          "output": "output_demultiplexer",
          "output_falco": "output_falco",
-          "output_multiqc": "output_multiqc"
+          "output_multiqc": "output_multiqc",
+          "output_run_information": "run_information",
        ]
      )

--- a/src/demultiplex/test.nf
+++ b/src/demultiplex/test.nf
@@ -35,6 +35,26 @@ workflow test_illumina {
      fastq_files.each{
        assert it.length() != 0: "Expected FASTQ file to not be empty"
      }
+      assert state.output_run_information.isFile(): "Expected output run information to be a file"
+      expected_run_information = """[Header]
+                                   |Date,6/24/2020
+                                   |Application,Illumina DRAGEN COVIDSeq Test Pipeline
+                                   |Instrument Type,NovaSeq6000
+                                   |Assay,Illumina COVIDSeq Test
+                                   |Index Adapters,IDT-ILMN DNA-RNA UDP Indexes
+                                   |Chemistry,Amplicon
+
+                                   |[Settings]
+                                   |AdapterRead1,CTGTCTCTTATACACATCT
+
+                                   |[Data]
+                                   |Lane,Sample_ID,Sample_Type,Index_ID,Index,Index2
+                                   |1,Sample1,PatientSample,UDP0001,GAACTGAGCG,TCGTGGAGCG
+                                   |1,SampleA,PatientSample,UDP0002,AGGTCAGATA,CTACAAGATA
+                                   |1,Sample23,PatientSample,UDP0003,CGTCTCATAT,TATAGTAGCT
+                                   |1,sampletest,PatientSample,UDP0004,ATTCCATAAG,TGCCTGGTGG
+                                   |""".stripMargin()
+      assert state.output_run_information.text.replaceAll("\r\n", "\n") == expected_run_information
    }
 }

--- a/src/io/publish/code.sh
+++ b/src/io/publish/code.sh
@@ -1,30 +1,26 @@
 #!/bin/bash

-echo "Publishing $par_input -> $par_output"
-echo "Publishing $par_input_falco -> $par_output_falco"
-echo "Publishing $par_input_multiqc -> $par_output_multiqc"
+set -eo pipefail

-echo
-echo "Creating directory if it does not exist:"
-mkdir -p $(dirname "$par_output") && echo "Containing directory $par_output created"
-mkdir -p $(dirname "$par_output_falco") && echo "Containing directory $par_output_falco created"
-mkdir -p $(dirname "$par_output_multiqc") && echo "Containing directory $par_output_multiqc created"
+declare -A input_output_mapping=(["par_input"]="par_output" 
+                                 ["par_input_falco"]="par_output_falco" 
+                                 ["par_input_multiqc"]="par_output_multiqc"
+                                 ["par_input_run_information"]="par_output_run_information"
+                                )

-echo
-echo "Copying files..."
-cp -rL "$par_input" "$par_output"
-cp -rL "$par_input_falco" "$par_output_falco"
-cp -rL "$par_input_multiqc" "$par_output_multiqc"
+for input_argument_name in "${!input_output_mapping[@]}"
+do
+    input_location="${!input_argument_name}"
+    output_argument_name="${input_output_mapping[$input_argument_name]}"
+    output_location="${!output_argument_name}"
+    echo "Publishing $input_location -> $output_location"

-echo
-echo "Output files:"
-echo "par_output:"
-ls "$par_output"
+    echo "Creating directory if it does not exist."
+    mkdir -p $(dirname "$output_location") && echo "Containing directory $output_location created"

-echo
-echo "par_output_falco:"
-ls "$par_output_falco"
+    echo "Copying files..."
+    cp -rL "$input_location" "$output_location"

-echo
-echo "par_output_multiqc:"
-ls "$par_output_multiqc"
+    echo "Output files for $output_location:"
+    ls "$output_location"
+done
--- a/src/io/publish/config.vsh.yaml
+++ b/src/io/publish/config.vsh.yaml
@@ -13,7 +13,11 @@ argument_groups:
        type: file
        required: true
      - name: "--input_multiqc"
-        description: Directory to write falco output to
+        description: Location where to write the MultiQC report to.
+        type: file
+        required: true
+      - name: "--input_run_information"
+        description: "Location where to write the run information to."
        type: file
        required: true
  - name: Output arguments
@@ -30,6 +34,10 @@ argument_groups:
        type: file
        direction: output
        default: "qc/multiqc_report.html"
+      - name: --output_run_information
+        type: file
+        direction: output
+        default: run_information.csv

 resources:
  - type: bash_script
--- a/src/runner/config.vsh.yaml
+++ b/src/runner/config.vsh.yaml
@@ -4,7 +4,10 @@ argument_groups:
  - name: Input arguments
    arguments:
      - name: --input
-        description: Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/`
+        description: |
+          Base directory of the canonical form `s3://<bucket>/<path>/<RunID>/`.
+          A tarball (tar.gz, .tgz, .tar) containing run information can be provided in which
+          case the RunID is set to the name of the tarball without the extension.
        type: file
        required: true
      - name: --run_information
@@ -27,15 +30,10 @@ argument_groups:
          required.
  - name: Annotation flags
    arguments:
-      - name: --add_date_time
+      - name: --plain_output
        description: |
-          Add date and time to the output directory name. This is useful
-          when running the same pipeline multiple times on the same input
-          directory.
-        type: boolean_true
-      - name: --add_workflow_id
-        description: |
-          Add a workflow identifier to the output directory name.
+          Flag to indicate that the output should be stored directly under $publish_dir rather than
+          under a subdirectory structure runID/<date_time>_demultiplex_<version>/.
        type: boolean_true
  - name: Output arguments
    arguments:
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -9,29 +9,46 @@ workflow run_wf {

  main:
    output_ch = input_ch
+      // Extract the ID from the input.
+      // If the input is a tarball, strip the suffix.
+      | map{ id, state ->
+        def id_with_suffix = state.input.getFileName().toString()
+        [
+          id,
+          state + [ run_id: id_with_suffix - ~/\.(tar.gz|tgz|tar)$/ ]
+        ]
+      }
      | demultiplex.run(
-        fromState: [
-          "input": "input",
-          "run_information": "run_information",
-          "demultiplexer": "demultiplexer",
-          "output": "fastq",
-          "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html"
-        ],
+        fromState: { id, state ->
+          def state_to_pass = [
+            "input": state.input,
+            "run_information": state.run_information,
+            "demultiplexer": state.demultiplexer,
+            "output": "fastq",
+            "output_falco": "qc/fastqc",
+            "output_multiqc": "qc/multiqc_report.html",
+          ]
+          if (state.run_information) {
+            state_to_pass += ["output_run_information": state.run_information.getName()] 
+          }
+          state_to_pass
+        },
        toState: { id, result, state ->
          state + result
        },
      )
      | publish.run(
        fromState: { id, state ->
-          def id1 = (params.add_date_time) ? "${id}_${date}" : id
-          def id2 = (params.add_workflow_id) ? "${id1}_demultiplex_${version}" : id1
+          println(state.plain_output)
+          def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
+          def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"

-          def fastq_output_1 = (id == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
-          def falco_output_1 = (id == "run") ? state.falco_output : "${id2}/" + state.falco_output
-          def multiqc_output_1 = (id == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
+          def fastq_output_1 = (id2 == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
+          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()}"

-          if (id == "run") {
+          if (id2 == "run") {
            println("Publising to ${params.publish_dir}")
          } else {
            println("Publising to ${params.publish_dir}/${id2}")
@@ -41,9 +58,11 @@ workflow run_wf {
            input: state.output,
            input_falco: state.output_falco,
            input_multiqc: state.output_multiqc,
+            input_run_information: state.output_run_information,
            output: fastq_output_1,
            output_falco: falco_output_1,
-            output_multiqc: multiqc_output_1
+            output_multiqc: multiqc_output_1,
+            output_run_information: run_information_output_1,
          ]
        },
        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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -116,7 +116,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -141,12 +141,12 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -160,7 +160,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  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 v0.3.1
+# interop_summary_to_csv v0.3.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.3.1"
+  echo "interop_summary_to_csv v0.3.3"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -470,10 +470,10 @@ 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="2024-12-11T15:30:29Z"
+LABEL org.opencontainers.image.created="2024-12-19T15:42:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
+LABEL org.opencontainers.image.version="v0.3.3"

 VIASHDOCKER
  fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.3.1"
+            echo "interop_summary_to_csv v0.3.3"
            exit
            ;;
        --input)
@@ -733,7 +733,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.3'
  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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -26,7 +26,17 @@ argument_groups:
    multiple_sep: ";"
  - type: "file"
    name: "--input_multiqc"
-    description: "Directory to write falco output to"
+    description: "Location where to write the MultiQC report to."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_run_information"
+    description: "Location where to write the run information to."
    info: null
    must_exist: true
    create_parent: true
@@ -69,6 +79,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--output_run_information"
+    info: null
+    default:
+    - "run_information.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
  path: "code.sh"
@@ -152,7 +173,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -170,12 +191,12 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -189,7 +210,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish v0.3.1
+# publish v0.3.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.3.1"
+  echo "publish v0.3.3"
  echo ""
  echo "Publish the processed results of the run"
  echo ""
@@ -186,7 +186,11 @@ function ViashHelp {
  echo ""
  echo "    --input_multiqc"
  echo "        type: file, required parameter, file must exist"
-  echo "        Directory to write falco output to"
+  echo "        Location where to write the MultiQC report to."
+  echo ""
+  echo "    --input_run_information"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Location where to write the run information to."
  echo ""
  echo "Output arguments:"
  echo "    --output"
@@ -200,6 +204,10 @@ function ViashHelp {
  echo "    --output_multiqc"
  echo "        type: file, output, file must exist"
  echo "        default: qc/multiqc_report.html"
+  echo ""
+  echo "    --output_run_information"
+  echo "        type: file, output, file must exist"
+  echo "        default: run_information.csv"
 }

 # initialise variables
@@ -482,10 +490,10 @@ 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="2024-12-11T15:30:29Z"
+LABEL org.opencontainers.image.created="2024-12-19T15:42:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
+LABEL org.opencontainers.image.version="v0.3.3"

 VIASHDOCKER
  fi
@@ -621,7 +629,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish v0.3.1"
+            echo "publish v0.3.3"
            exit
            ;;
        --input)
@@ -657,6 +665,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_INPUT_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --input_run_information)
+            [ -n "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && ViashError Bad arguments for option \'--input_run_information\': \'$VIASH_PAR_INPUT_RUN_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_RUN_INFORMATION="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_run_information. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --input_run_information=*)
+            [ -n "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && ViashError Bad arguments for option \'--input_run_information=*\': \'$VIASH_PAR_INPUT_RUN_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_RUN_INFORMATION=$(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"
@@ -690,6 +709,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_OUTPUT_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --output_run_information)
+            [ -n "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && ViashError Bad arguments for option \'--output_run_information\': \'$VIASH_PAR_OUTPUT_RUN_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_RUN_INFORMATION="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_run_information. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --output_run_information=*)
+            [ -n "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && ViashError Bad arguments for option \'--output_run_information=*\': \'$VIASH_PAR_OUTPUT_RUN_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
@@ -778,7 +808,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.3'
  fi

  # print dockerfile
@@ -874,6 +904,10 @@ if [ -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then
  ViashError '--input_multiqc' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
 fi
+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_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
@@ -909,6 +943,9 @@ fi
 if [ -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then
  VIASH_PAR_OUTPUT_MULTIQC="qc/multiqc_report.html"
 fi
+if [ -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then
+  VIASH_PAR_OUTPUT_RUN_INFORMATION="run_information.csv"
+fi

 # check whether required files exist
 if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -923,6 +960,10 @@ if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ] && [ ! -e "$VIASH_PAR_INPUT_MULTIQC" ]; t
  ViashError "Input file '$VIASH_PAR_INPUT_MULTIQC' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
+  ViashError "Input file '$VIASH_PAR_INPUT_RUN_INFORMATION' does not exist."
+  exit 1
+fi

 # check whether parameters values are of the right type
 if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -1008,6 +1049,9 @@ fi
 if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_MULTIQC")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_MULTIQC")"
 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  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  if [ "$VIASH_MODE" == "run" ]; then
@@ -1033,6 +1077,10 @@ if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_MULTIQC")" )
  VIASH_PAR_INPUT_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_MULTIQC")
 fi
+if [ ! -z "$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 "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
@@ -1048,6 +1096,11 @@ if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ]; then
  VIASH_PAR_OUTPUT_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_MULTIQC")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_MULTIQC" )
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_RUN_INFORMATION")" )
+  VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_RUN_INFORMATION" )
+fi
 if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1120,9 +1173,11 @@ cat > "\$tempscript" << 'VIASHMAIN'
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
 $( 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 ${VIASH_PAR_OUTPUT+x} ]; then echo "${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 ${VIASH_META_NAME+x} ]; then echo "${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 )
@@ -1145,34 +1200,30 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 ## VIASH END
 #!/bin/bash

-echo "Publishing \$par_input -> \$par_output"
-echo "Publishing \$par_input_falco -> \$par_output_falco"
-echo "Publishing \$par_input_multiqc -> \$par_output_multiqc"
+set -eo pipefail

-echo
-echo "Creating directory if it does not exist:"
-mkdir -p \$(dirname "\$par_output") && echo "Containing directory \$par_output created"
-mkdir -p \$(dirname "\$par_output_falco") && echo "Containing directory \$par_output_falco created"
-mkdir -p \$(dirname "\$par_output_multiqc") && echo "Containing directory \$par_output_multiqc created"
+declare -A input_output_mapping=(["par_input"]="par_output" 
+                                 ["par_input_falco"]="par_output_falco" 
+                                 ["par_input_multiqc"]="par_output_multiqc"
+                                 ["par_input_run_information"]="par_output_run_information"
+                                )

-echo
-echo "Copying files..."
-cp -rL "\$par_input" "\$par_output"
-cp -rL "\$par_input_falco" "\$par_output_falco"
-cp -rL "\$par_input_multiqc" "\$par_output_multiqc"
+for input_argument_name in "\${!input_output_mapping[@]}"
+do
+    input_location="\${!input_argument_name}"
+    output_argument_name="\${input_output_mapping[\$input_argument_name]}"
+    output_location="\${!output_argument_name}"
+    echo "Publishing \$input_location -> \$output_location"

-echo
-echo "Output files:"
-echo "par_output:"
-ls "\$par_output"
+    echo "Creating directory if it does not exist."
+    mkdir -p \$(dirname "\$output_location") && echo "Containing directory \$output_location created"

-echo
-echo "par_output_falco:"
-ls "\$par_output_falco"
+    echo "Copying files..."
+    cp -rL "\$input_location" "\$output_location"

-echo
-echo "par_output_multiqc:"
-ls "\$par_output_multiqc"
+    echo "Output files for \$output_location:"
+    ls "\$output_location"
+done
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"
@@ -1192,6 +1243,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ]; then
    VIASH_PAR_INPUT_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_MULTIQC")
  fi
+  if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
+    VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_RUN_INFORMATION")
+  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
@@ -1201,6 +1255,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ]; then
    VIASH_PAR_OUTPUT_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_MULTIQC")
  fi
+  if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
+    VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
+  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
@@ -1229,6 +1286,10 @@ if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ] && [ ! -e "$VIASH_PAR_OUTPUT_MULTIQC" ];
  ViashError "Output file '$VIASH_PAR_OUTPUT_MULTIQC' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
+  ViashError "Output file '$VIASH_PAR_OUTPUT_RUN_INFORMATION' 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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -130,7 +130,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -148,12 +148,12 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -167,7 +167,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# untar v0.3.1
+# untar v0.3.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.1"
+  echo "untar v0.3.3"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -476,10 +476,10 @@ 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="2024-12-11T15:30:29Z"
+LABEL org.opencontainers.image.created="2024-12-19T15:42:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
+LABEL org.opencontainers.image.version="v0.3.3"

 VIASHDOCKER
  fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.1"
+            echo "untar v0.3.3"
            exit
            ;;
        --input)
@@ -745,7 +745,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.3'
  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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -139,12 +139,12 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -158,7 +158,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.3.1
+// combine_samples v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2972,13 +2972,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2995,7 +2995,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "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 = 'v0.3.1'
+  version = 'v0.3.3'
  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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -133,12 +133,12 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -152,7 +152,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.1
+// gather_fastqs_and_validate v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2965,13 +2965,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2988,7 +2988,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3063,7 +3063,10 @@ workflow run_wf {
              println "Found sample names column '${csv_items[sample_id_column_index]}'."
              return
            }
-            samples += csv_items[sample_id_column_index]
+            def candidate_sample_id = csv_items[sample_id_column_index]
+            if (candidate_sample_id?.trim()) { // Don't add empty csv entries.
+              samples += csv_items[sample_id_column_index]
+            }
          }
          // This return is important! (If 'true' is returned, the parsing stops.)
          return 
--- 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 = 'v0.3.1'
+  version = 'v0.3.3'
  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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -85,6 +85,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--output_run_information"
+    info: null
+    default:
+    - "$id/run_information.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "nextflow_script"
  path: "main.nf"
@@ -220,9 +231,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -234,7 +245,7 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -248,7 +259,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.3.1
+// demultiplex v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "demultiplex",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2900,6 +2900,19 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--output_run_information",
+          "default" : [
+            "$id/run_information.csv"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    }
@@ -3088,13 +3101,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3111,7 +3124,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3369,7 +3382,8 @@ workflow run_wf {
          //"_meta": "_meta",
          "output": "output_demultiplexer",
          "output_falco": "output_falco",
-          "output_multiqc": "output_multiqc"
+          "output_multiqc": "output_multiqc",
+          "output_run_information": "run_information",
        ]
      )

--- 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 = 'v0.3.1'
+  version = 'v0.3.3'
  description = 'Demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/demultiplex/nextflow_schema.json
+++ b/target/nextflow/demultiplex/nextflow_schema.json
@@ -98,6 +98,17 @@
            }
    

+        ,
+                "output_run_information": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output_run_information.csv`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_run_information.csv`. "
+            ,
+                "default":"$id.$key.output_run_information.csv"
+            }
+    
+
 }
 },
    
--- 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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -116,7 +116,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -141,12 +141,12 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -160,7 +160,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  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 v0.3.1
+// interop_summary_to_csv v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "interop_summary_to_csv",
  "namespace" : "io",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2947,7 +2947,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2977,13 +2977,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3000,7 +3000,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3423,7 +3423,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.3"
  },
  "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 = 'v0.3.1'
+  version = 'v0.3.3'
 }

 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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -26,7 +26,17 @@ argument_groups:
    multiple_sep: ";"
  - type: "file"
    name: "--input_multiqc"
-    description: "Directory to write falco output to"
+    description: "Location where to write the MultiQC report to."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_run_information"
+    description: "Location where to write the run information to."
    info: null
    must_exist: true
    create_parent: true
@@ -69,6 +79,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--output_run_information"
+    info: null
+    default:
+    - "run_information.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
  path: "code.sh"
@@ -152,7 +173,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -170,12 +191,12 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -189,7 +210,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.3.1
+// publish v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish",
  "namespace" : "io",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2836,7 +2836,18 @@ meta = [
        {
          "type" : "file",
          "name" : "--input_multiqc",
-          "description" : "Directory to write falco output to",
+          "description" : "Location where to write the MultiQC report to.",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--input_run_information",
+          "description" : "Location where to write the run information to.",
          "must_exist" : true,
          "create_parent" : true,
          "required" : true,
@@ -2887,6 +2898,19 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--output_run_information",
+          "default" : [
+            "run_information.csv"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    }
@@ -2989,7 +3013,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3012,13 +3036,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3035,7 +3059,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3067,9 +3091,11 @@ cat > "$tempscript" << VIASHMAIN
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
 $( 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 ${VIASH_PAR_OUTPUT+x} ]; then echo "${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 ${VIASH_META_NAME+x} ]; then echo "${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 )
@@ -3092,34 +3118,30 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 ## VIASH END
 #!/bin/bash

-echo "Publishing \\$par_input -> \\$par_output"
-echo "Publishing \\$par_input_falco -> \\$par_output_falco"
-echo "Publishing \\$par_input_multiqc -> \\$par_output_multiqc"
+set -eo pipefail

-echo
-echo "Creating directory if it does not exist:"
-mkdir -p \\$(dirname "\\$par_output") && echo "Containing directory \\$par_output created"
-mkdir -p \\$(dirname "\\$par_output_falco") && echo "Containing directory \\$par_output_falco created"
-mkdir -p \\$(dirname "\\$par_output_multiqc") && echo "Containing directory \\$par_output_multiqc created"
+declare -A input_output_mapping=(["par_input"]="par_output" 
+                                 ["par_input_falco"]="par_output_falco" 
+                                 ["par_input_multiqc"]="par_output_multiqc"
+                                 ["par_input_run_information"]="par_output_run_information"
+                                )

-echo
-echo "Copying files..."
-cp -rL "\\$par_input" "\\$par_output"
-cp -rL "\\$par_input_falco" "\\$par_output_falco"
-cp -rL "\\$par_input_multiqc" "\\$par_output_multiqc"
+for input_argument_name in "\\${!input_output_mapping[@]}"
+do
+    input_location="\\${!input_argument_name}"
+    output_argument_name="\\${input_output_mapping[\\$input_argument_name]}"
+    output_location="\\${!output_argument_name}"
+    echo "Publishing \\$input_location -> \\$output_location"

-echo
-echo "Output files:"
-echo "par_output:"
-ls "\\$par_output"
+    echo "Creating directory if it does not exist."
+    mkdir -p \\$(dirname "\\$output_location") && echo "Containing directory \\$output_location created"

-echo
-echo "par_output_falco:"
-ls "\\$par_output_falco"
+    echo "Copying files..."
+    cp -rL "\\$input_location" "\\$output_location"

-echo
-echo "par_output_multiqc:"
-ls "\\$par_output_multiqc"
+    echo "Output files for \\$output_location:"
+    ls "\\$output_location"
+done
 VIASHMAIN
 bash "$tempscript"
 '''
@@ -3481,7 +3503,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.3"
  },
  "tag" : "$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 = 'v0.3.1'
+  version = 'v0.3.3'
  description = 'Publish the processed results of the run'
 }

--- a/target/nextflow/io/publish/nextflow_schema.json
+++ b/target/nextflow/io/publish/nextflow_schema.json
@@ -37,8 +37,18 @@
                "input_multiqc": {
                "type":
                "string",
-                "description": "Type: `file`, required. Directory to write falco output to",
-                "help_text": "Type: `file`, required. Directory to write falco output to"
+                "description": "Type: `file`, required. Location where to write the MultiQC report to",
+                "help_text": "Type: `file`, required. Location where to write the MultiQC report to."
+            
+            }
+    
+
+        ,
+                "input_run_information": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. Location where to write the run information to",
+                "help_text": "Type: `file`, required. Location where to write the run information to."
            
            }
    
@@ -86,6 +96,17 @@
            }
    

+        ,
+                "output_run_information": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_run_information.csv`. ",
+                "help_text": "Type: `file`, default: `$id.$key.output_run_information.csv`. "
+            ,
+                "default":"$id.$key.output_run_information.csv"
+            }
+    
+
 }
 },
    
--- 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: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -130,7 +130,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -148,12 +148,12 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -167,7 +167,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.3.1
+// untar v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
  "namespace" : "io",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2966,7 +2966,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2989,13 +2989,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3012,7 +3012,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3465,7 +3465,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.3"
  },
  "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 = 'v0.3.1'
+  version = 'v0.3.3'
  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
@@ -1,11 +1,13 @@
 name: "runner"
-version: "v0.3.1"
+version: "v0.3.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
  - type: "file"
    name: "--input"
-    description: "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/`"
+    description: "Base directory of the canonical form `s3://<bucket>/<path>/<RunID>/`.\n\
+      A tarball (tar.gz, .tgz, .tar) containing run information can be provided in\
+      \ which\ncase the RunID is set to the name of the tarball without the extension.\n"
    info: null
    must_exist: true
    create_parent: true
@@ -42,14 +44,9 @@ argument_groups:
 - name: "Annotation flags"
  arguments:
  - type: "boolean_true"
-    name: "--add_date_time"
-    description: "Add date and time to the output directory name. This is useful\n\
-      when running the same pipeline multiple times on the same input\ndirectory.\n"
-    info: null
-    direction: "input"
-  - type: "boolean_true"
-    name: "--add_workflow_id"
-    description: "Add a workflow identifier to the output directory name.\n"
+    name: "--plain_output"
+    description: "Flag to indicate that the output should be stored directly under\
+      \ $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n"
    info: null
    direction: "input"
 - name: "Output arguments"
@@ -182,15 +179,15 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
-  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.0-4-g35e1ab8"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.3.1"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -204,7 +201,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.3.1
+// runner v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "runner",
-  "version" : "v0.3.1",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2813,7 +2813,7 @@ meta = [
        {
          "type" : "file",
          "name" : "--input",
-          "description" : "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/`",
+          "description" : "Base directory of the canonical form `s3://<bucket>/<path>/<RunID>/`.\nA tarball (tar.gz, .tgz, .tar) containing run information can be provided in which\ncase the RunID is set to the name of the tarball without the extension.\n",
          "must_exist" : true,
          "create_parent" : true,
          "required" : true,
@@ -2852,14 +2852,8 @@ meta = [
      "arguments" : [
        {
          "type" : "boolean_true",
-          "name" : "--add_date_time",
-          "description" : "Add date and time to the output directory name. This is useful\nwhen running the same pipeline multiple times on the same input\ndirectory.\n",
-          "direction" : "input"
-        },
-        {
-          "type" : "boolean_true",
-          "name" : "--add_workflow_id",
-          "description" : "Add a workflow identifier to the output directory name.\n",
+          "name" : "--plain_output",
+          "description" : "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
          "direction" : "input"
        }
      ]
@@ -3027,13 +3021,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
-    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.0-4-g35e1ab8"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.1",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3050,7 +3044,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3086,29 +3080,46 @@ workflow run_wf {

  main:
    output_ch = input_ch
+      // Extract the ID from the input.
+      // If the input is a tarball, strip the suffix.
+      | map{ id, state ->
+        def id_with_suffix = state.input.getFileName().toString()
+        [
+          id,
+          state + [ run_id: id_with_suffix - ~/\.(tar.gz|tgz|tar)$/ ]
+        ]
+      }
      | demultiplex.run(
-        fromState: [
-          "input": "input",
-          "run_information": "run_information",
-          "demultiplexer": "demultiplexer",
-          "output": "fastq",
-          "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html"
-        ],
+        fromState: { id, state ->
+          def state_to_pass = [
+            "input": state.input,
+            "run_information": state.run_information,
+            "demultiplexer": state.demultiplexer,
+            "output": "fastq",
+            "output_falco": "qc/fastqc",
+            "output_multiqc": "qc/multiqc_report.html",
+          ]
+          if (state.run_information) {
+            state_to_pass += ["output_run_information": state.run_information.getName()] 
+          }
+          state_to_pass
+        },
        toState: { id, result, state ->
          state + result
        },
      )
      | publish.run(
        fromState: { id, state ->
-          def id1 = (params.add_date_time) ? "${id}_${date}" : id
-          def id2 = (params.add_workflow_id) ? "${id1}_demultiplex_${version}" : id1
+          println(state.plain_output)
+          def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
+          def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"

-          def fastq_output_1 = (id == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
-          def falco_output_1 = (id == "run") ? state.falco_output : "${id2}/" + state.falco_output
-          def multiqc_output_1 = (id == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
+          def fastq_output_1 = (id2 == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
+          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()}"

-          if (id == "run") {
+          if (id2 == "run") {
            println("Publising to ${params.publish_dir}")
          } else {
            println("Publising to ${params.publish_dir}/${id2}")
@@ -3118,9 +3129,11 @@ workflow run_wf {
            input: state.output,
            input_falco: state.output_falco,
            input_multiqc: state.output_multiqc,
+            input_run_information: state.output_run_information,
            output: fastq_output_1,
            output_falco: falco_output_1,
-            output_multiqc: multiqc_output_1
+            output_multiqc: multiqc_output_1,
+            output_run_information: run_information_output_1,
          ]
        },
        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 = 'v0.3.1'
+  version = 'v0.3.3'
  description = 'Runner for demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/runner/nextflow_schema.json
+++ b/target/nextflow/runner/nextflow_schema.json
@@ -17,8 +17,8 @@
                "input": {
                "type":
                "string",
-                "description": "Type: `file`, required. Base directory of the form `s3:/\u003cbucket\u003e/Sequencing/\u003cSequencer\u003e/\u003cRunID\u003e/`",
-                "help_text": "Type: `file`, required. Base directory of the form `s3:/\u003cbucket\u003e/Sequencing/\u003cSequencer\u003e/\u003cRunID\u003e/`"
+                "description": "Type: `file`, required. Base directory of the canonical form `s3://\u003cbucket\u003e/\u003cpath\u003e/\u003cRunID\u003e/`",
+                "help_text": "Type: `file`, required. Base directory of the canonical form `s3://\u003cbucket\u003e/\u003cpath\u003e/\u003cRunID\u003e/`.\nA tarball (tar.gz, .tgz, .tar) containing run information can be provided in which\ncase the RunID is set to the name of the tarball without the extension.\n"
            
            }
    
@@ -56,22 +56,11 @@
    "properties": {
    
        
-                "add_date_time": {
+                "plain_output": {
                "type":
                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Add date and time to the output directory name",
-                "help_text": "Type: `boolean_true`, default: `false`. Add date and time to the output directory name. This is useful\nwhen running the same pipeline multiple times on the same input\ndirectory.\n"
-            ,
-                "default":false
-            }
-    
-
-        ,
-                "add_workflow_id": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Add a workflow identifier to the output directory name",
-                "help_text": "Type: `boolean_true`, default: `false`. Add a workflow identifier to the output directory name.\n"
+                "description": "Type: `boolean_true`, default: `false`. Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/\u003cdate_time\u003e_demultiplex_\u003cversion\u003e/",
+                "help_text": "Type: `boolean_true`, default: `false`. Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/\u003cdate_time\u003e_demultiplex_\u003cversion\u003e/.\n"
            ,
                "default":false
            }