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 · 2024-12-11 15:46:01 +00:00
40 changed files with 720 additions and 309 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,76 @@
+# 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
+
+* Add `--run_information` and `--demultiplexer` arguments to `runner` workflow (PR #27).
+
+# Bug fixes
+
+* Fix detection of sample IDs from Illumina V2 sample sheets (PR #28).
+
+* Provide a clear error message when `--run_information` is provided but not `--demultiplexer` (PR #27).
+
 # demultiplex v0.3.0

 ## Major updates
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.0
+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
@@ -29,9 +29,9 @@ workflow run_wf {
              println "Encountered next header '[${start_parsing}]', stopping parsing."
              return true
            }
-            // [Data] for illumina
+            // [Data], [BCLConvert_Data] for illumina
            // [Samples] for Element Biosciences
-            if (header in ["Data", "Samples"]) {
+            if (header in ["Data", "Samples", "BCLConvert_Data"]) {
              println "Found header [${header}], start parsing."
              start_parsing = true
              return
@@ -50,13 +50,16 @@ 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 
        }
        assert start_parsing: 
-          "Sample information file does not contain [Data] or [Samples] header!"
+          "Sample information file does not contain [Data], [Samples] or [BCLConvert_Data] header!"
        assert samples.size() > 1:
          "Sample information file does not seem to contain any information about the samples!"
        println "Finished processing run information file, found samples: ${samples}."
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -48,6 +48,11 @@ argument_groups:
        direction: output
        required: false
        default: "$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
@@ -25,6 +25,11 @@ workflow run_wf {
      | map {id, state ->
        def newState = [:]
        println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
+        // No auto-detection of run information file (it is user provided),
+        // in this case the demultiplexer should also be specified.
+        assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
+          "you must also provide a demultiplexer"
+
        if (!state.run_information) {
          println("Run information was not specified, auto-detecting...")
          // The supported_platforms hashmap must be a 1-on-1 mapping
@@ -62,7 +67,7 @@ workflow run_wf {
            "found in input directory."

          // When autodetecting, the demultiplexer must be set if the run information was found
-          assert demultiplexer, "State error: the demultiplexer should have been autodetected. " +
+          assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
            "Please report this as a bug."

          // When autodetecting, the found demultiplexer must match
@@ -82,7 +87,7 @@ workflow run_wf {
            "run_information": run_information,
            "demultiplexer": demultiplexer,
          ]
-        }
+        } // end auto-detection logic

        if (newState.demultiplexer in ["bclconvert"]) {
          // Do not add InterOp to state because we generate the summary csv's in the next
@@ -220,7 +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
@@ -4,20 +4,36 @@ 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
+        description: |
+          CSV file containing sample information, which will be used as 
+          input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)
+          or 'RunManifest.csv' (Element Biosciences). If not specified,
+          will try to autodetect the sample sheet in the input directory.
+          Requires --demultiplexer to be set.
+        type: file
+        required: false
+      - name: "--demultiplexer"
+        type: string
+        required: false
+        choices: ["bases2fastq", "bclconvert"]
+        description: |
+          Demultiplexer to use, choice depends on the provider
+          of the instrument that was used to generate the data.
+          When not using --sample_sheet, specifying this argument is not
+          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
@@ -9,27 +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)$/ ]
+        ]
+      }
      | demultiplex.run(
-        fromState: [
-          "input": "input",
-          "output": "fastq",
-          "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html",
-        ],
+        fromState: { id, state ->
+          def state_to_pass = [
+            "input": state.input,
+            "run_information": state.run_information,
+            "demultiplexer": state.demultiplexer,
+            "output": "fastq",
+            "output_falco": "qc/fastqc",
+            "output_multiqc": "qc/multiqc_report.html",
+          ]
+          if (state.run_information) {
+            state_to_pass += ["output_run_information": state.run_information.getName()] 
+          }
+          state_to_pass
+        },
        toState: { id, result, state ->
          state + result
        },
      )
      | publish.run(
        fromState: { id, state ->
-          def id1 = (params.add_date_time) ? "${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}")
@@ -39,9 +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: "v0.3.0"
+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: "v0.3.0"
+  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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  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 := 'v0.3.0'"
+  - ".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 v0.3.0
+# 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 v0.3.0"
+  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="2024-12-11T09:19:38Z"
+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="c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
+LABEL org.opencontainers.image.version="v0.3.3"

 VIASHDOCKER
  fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.3.0"
+            echo "interop_summary_to_csv v0.3.3"
            exit
            ;;
        --input)
@@ -733,7 +733,7 @@ if [[ "$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:v0.3.0'
+    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: "v0.3.0"
+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: "v0.3.0"
+  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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  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 := 'v0.3.0'"
+  - ".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 v0.3.0
+# 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 v0.3.0"
+  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="2024-12-11T09:19:38Z"
+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="c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-LABEL org.opencontainers.image.version="v0.3.0"
+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 v0.3.0"
+            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:v0.3.0'
+    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: "v0.3.0"
+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: "v0.3.0"
+  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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  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 := 'v0.3.0'"
+  - ".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 v0.3.0
+# 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 v0.3.0"
+  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="2024-12-11T09:19:39Z"
+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="c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
+LABEL org.opencontainers.image.version="v0.3.3"

 VIASHDOCKER
  fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.0"
+            echo "untar v0.3.3"
            exit
            ;;
        --input)
@@ -745,7 +745,7 @@ if [[ "$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:v0.3.0'
+    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: "v0.3.0"
+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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -158,7 +158,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.3.0
+// combine_samples v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.3.0",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2972,13 +2972,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2995,7 +2995,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".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 = 'v0.3.0'
+  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: "v0.3.0"
+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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -152,7 +152,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.0
+// gather_fastqs_and_validate v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.3.0",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2965,13 +2965,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2988,7 +2988,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3042,9 +3042,9 @@ workflow run_wf {
              println "Encountered next header '[${start_parsing}]', stopping parsing."
              return true
            }
-            // [Data] for illumina
+            // [Data], [BCLConvert_Data] for illumina
            // [Samples] for Element Biosciences
-            if (header in ["Data", "Samples"]) {
+            if (header in ["Data", "Samples", "BCLConvert_Data"]) {
              println "Found header [${header}], start parsing."
              start_parsing = true
              return
@@ -3063,13 +3063,16 @@ 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 
        }
        assert start_parsing: 
-          "Sample information file does not contain [Data] or [Samples] header!"
+          "Sample information file does not contain [Data], [Samples] or [BCLConvert_Data] header!"
        assert samples.size() > 1:
          "Sample information file does not seem to contain any information about the samples!"
        println "Finished processing run information file, found samples: ${samples}."
--- 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 = 'v0.3.0'
+  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: "v0.3.0"
+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:
+    - "$id/run_information.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "nextflow_script"
  path: "main.nf"
@@ -220,9 +231,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -234,7 +245,7 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
  name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -248,7 +259,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".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 v0.3.0
+// 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" : "v0.3.0",
+  "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" : [
+            "$id/run_information.csv"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    }
@@ -3088,13 +3101,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3111,7 +3124,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3169,6 +3182,11 @@ workflow run_wf {
      | map {id, state ->
        def newState = [:]
        println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
+        // No auto-detection of run information file (it is user provided),
+        // in this case the demultiplexer should also be specified.
+        assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
+          "you must also provide a demultiplexer"
+
        if (!state.run_information) {
          println("Run information was not specified, auto-detecting...")
          // The supported_platforms hashmap must be a 1-on-1 mapping
@@ -3206,7 +3224,7 @@ workflow run_wf {
            "found in input directory."

          // When autodetecting, the demultiplexer must be set if the run information was found
-          assert demultiplexer, "State error: the demultiplexer should have been autodetected. " +
+          assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
            "Please report this as a bug."

          // When autodetecting, the found demultiplexer must match
@@ -3226,7 +3244,7 @@ workflow run_wf {
            "run_information": run_information,
            "demultiplexer": demultiplexer,
          ]
-        }
+        } // end auto-detection logic

        if (newState.demultiplexer in ["bclconvert"]) {
          // Do not add InterOp to state because we generate the summary csv's in the next
@@ -3364,7 +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 = 'v0.3.0'
+  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: "v0.3.0"
+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: "v0.3.0"
+  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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  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 := 'v0.3.0'"
+  - ".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 v0.3.0
+// 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" : "v0.3.0",
+  "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" : "v0.3.0",
+      "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" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "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" : "v0.3.0",
+    "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 := 'v0.3.0'"
+      ".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" : "v0.3.0"
+    "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 = 'v0.3.0'
+  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: "v0.3.0"
+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: "v0.3.0"
+  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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  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 := 'v0.3.0'"
+  - ".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 v0.3.0
+// 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" : "v0.3.0",
+  "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" : "v0.3.0",
+      "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" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "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" : "v0.3.0",
+    "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 := 'v0.3.0'"
+      ".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 "$tempscript"
 '''
@@ -3481,7 +3503,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.3"
  },
  "tag" : "$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 = 'v0.3.0'
+  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: "v0.3.0"
+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: "v0.3.0"
+  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: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  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: "v0.3.0"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -167,7 +167,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.3.0
+// untar v0.3.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
  "namespace" : "io",
-  "version" : "v0.3.0",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2966,7 +2966,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2989,13 +2989,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3012,7 +3012,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".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" : "v0.3.0"
+    "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 = 'v0.3.0'
+  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: "v0.3.0"
+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
@@ -13,17 +15,38 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--run_information"
+    description: "CSV file containing sample information, which will be used as \n\
+      input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\n\
+      or 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect\
+      \ the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--demultiplexer"
+    description: "Demultiplexer to use, choice depends on the provider\nof the instrument\
+      \ that was used to generate the data.\nWhen not using --sample_sheet, specifying\
+      \ this argument is not\nrequired.\n"
+    info: null
+    required: false
+    choices:
+    - "bases2fastq"
+    - "bclconvert"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - 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\
+      \ $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n"
    info: null
    direction: "input"
 - name: "Output arguments"
@@ -156,15 +179,15 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.2-4-ge297e8f"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -178,7 +201,7 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".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 v0.3.0
+// 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" : "v0.3.0",
+  "version" : "v0.3.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2813,13 +2813,37 @@ 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,
          "direction" : "input",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--run_information",
+          "description" : "CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\nor 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--demultiplexer",
+          "description" : "Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
+          "required" : false,
+          "choices" : [
+            "bases2fastq",
+            "bclconvert"
+          ],
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -2828,14 +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 $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
          "direction" : "input"
        }
      ]
@@ -3003,13 +3021,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.2-4-ge297e8f"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3026,7 +3044,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3062,27 +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)$/ ]
+        ]
+      }
      | demultiplex.run(
-        fromState: [
-          "input": "input",
-          "output": "fastq",
-          "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html",
-        ],
+        fromState: { id, state ->
+          def state_to_pass = [
+            "input": state.input,
+            "run_information": state.run_information,
+            "demultiplexer": state.demultiplexer,
+            "output": "fastq",
+            "output_falco": "qc/fastqc",
+            "output_multiqc": "qc/multiqc_report.html",
+          ]
+          if (state.run_information) {
+            state_to_pass += ["output_run_information": state.run_information.getName()] 
+          }
+          state_to_pass
+        },
        toState: { id, result, state ->
          state + result
        },
      )
      | publish.run(
        fromState: { id, state ->
-          def id1 = (params.add_date_time) ? "${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}")
@@ -3092,9 +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 = 'v0.3.0'
+  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 +17,30 @@
                "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"
+            
+            }
+    
+
+        ,
+                "run_information": {
+                "type":
+                "string",
+                "description": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer",
+                "help_text": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called \u0027SampleSheet.csv\u0027 (Illumina)\nor \u0027RunManifest.csv\u0027 (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
+            
+            }
+    
+
+        ,
+                "demultiplexer": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data",
+                "help_text": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
+                "enum": ["bases2fastq", "bclconvert"]
+            
            
            }
    
@@ -34,22 +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
            }