Build branch main with version main (798e361)

Build pipeline: viash-hub.demultiplex.main-plzkv

Source commit: 798e361afe

Source message: Add run information to output (#31)

CHANGELOG.md

@@ -19,6 +19,7 @@
     $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
@@ -48,6 +49,9 @@
 
 - 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
 

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

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",
         ]
       )
 

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
     }
 }
 

src/io/publish/code.sh

@@ -1,30 +1,26 @@
 #!/bin/bash
 
-echo "Publishing $par_input -> $par_output"
+set -eo pipefail
-echo "Publishing $par_input_falco -> $par_output_falco"
-echo "Publishing $par_input_multiqc -> $par_output_multiqc"
 
-echo
+declare -A input_output_mapping=(["par_input"]="par_output" 
-echo "Creating directory if it does not exist:"
+                                 ["par_input_falco"]="par_output_falco" 
-mkdir -p $(dirname "$par_output") && echo "Containing directory $par_output created"
+                                 ["par_input_multiqc"]="par_output_multiqc"
-mkdir -p $(dirname "$par_output_falco") && echo "Containing directory $par_output_falco created"
+                                 ["par_input_run_information"]="par_output_run_information"
-mkdir -p $(dirname "$par_output_multiqc") && echo "Containing directory $par_output_multiqc created"
+                                )
 
-echo
+for input_argument_name in "${!input_output_mapping[@]}"
-echo "Copying files..."
+do
-cp -rL "$par_input" "$par_output"
+    input_location="${!input_argument_name}"
-cp -rL "$par_input_falco" "$par_output_falco"
+    output_argument_name="${input_output_mapping[$input_argument_name]}"
-cp -rL "$par_input_multiqc" "$par_output_multiqc"
+    output_location="${!output_argument_name}"
+    echo "Publishing $input_location -> $output_location"
 
-echo
+    echo "Creating directory if it does not exist."
-echo "Output files:"
+    mkdir -p $(dirname "$output_location") && echo "Containing directory $output_location created"
-echo "par_output:"
-ls "$par_output"
 
-echo
+    echo "Copying files..."
-echo "par_output_falco:"
+    cp -rL "$input_location" "$output_location"
-ls "$par_output_falco"
 
-echo
+    echo "Output files for $output_location:"
-echo "par_output_multiqc:"
+    ls "$output_location"
-ls "$par_output_multiqc"
+done

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

src/runner/main.nf

@@ -19,14 +19,20 @@ workflow run_wf {
         ]
       }
       | demultiplex.run(
-        fromState: [
+        fromState: { id, state ->
-          "input": "input",
+          def state_to_pass = [
-          "run_information": "run_information",
+            "input": state.input,
-          "demultiplexer": "demultiplexer",
+            "run_information": state.run_information,
-          "output": "fastq",
+            "demultiplexer": state.demultiplexer,
-          "output_falco": "qc/fastqc",
+            "output": "fastq",
-          "output_multiqc": "qc/multiqc_report.html"
+            "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
         },
@@ -40,6 +46,7 @@ workflow run_wf {
           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 (id2 == "run") {
             println("Publising to ${params.publish_dir}")
@@ -51,9 +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 -> [:] },

target/executable/io/interop_summary_to_csv/.config.vsh.yaml

@@ -141,9 +141,9 @@ 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: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/executable/io/interop_summary_to_csv/interop_summary_to_csv

@@ -470,9 +470,9 @@ 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="2024-12-18T15:00:53Z"
+LABEL org.opencontainers.image.created="2024-12-19T15:39:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="8d3c2888d6df6688763d303dba03ce53d339fb0f"
+LABEL org.opencontainers.image.revision="798e361afeea8dbb84dc23ef38e4fbc3883463e7"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/io/publish/.config.vsh.yaml

@@ -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"
@@ -170,9 +191,9 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/executable/io/publish/publish

@@ -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
@@ -482,9 +490,9 @@ 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="2024-12-18T15:00:54Z"
+LABEL org.opencontainers.image.created="2024-12-19T15:39:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="8d3c2888d6df6688763d303dba03ce53d339fb0f"
+LABEL org.opencontainers.image.revision="798e361afeea8dbb84dc23ef38e4fbc3883463e7"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -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
@@ -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"
+set -eo pipefail
-echo "Publishing \$par_input_falco -> \$par_output_falco"
-echo "Publishing \$par_input_multiqc -> \$par_output_multiqc"
 
-echo
+declare -A input_output_mapping=(["par_input"]="par_output" 
-echo "Creating directory if it does not exist:"
+                                 ["par_input_falco"]="par_output_falco" 
-mkdir -p \$(dirname "\$par_output") && echo "Containing directory \$par_output created"
+                                 ["par_input_multiqc"]="par_output_multiqc"
-mkdir -p \$(dirname "\$par_output_falco") && echo "Containing directory \$par_output_falco created"
+                                 ["par_input_run_information"]="par_output_run_information"
-mkdir -p \$(dirname "\$par_output_multiqc") && echo "Containing directory \$par_output_multiqc created"
+                                )
 
-echo
+for input_argument_name in "\${!input_output_mapping[@]}"
-echo "Copying files..."
+do
-cp -rL "\$par_input" "\$par_output"
+    input_location="\${!input_argument_name}"
-cp -rL "\$par_input_falco" "\$par_output_falco"
+    output_argument_name="\${input_output_mapping[\$input_argument_name]}"
-cp -rL "\$par_input_multiqc" "\$par_output_multiqc"
+    output_location="\${!output_argument_name}"
+    echo "Publishing \$input_location -> \$output_location"
 
-echo
+    echo "Creating directory if it does not exist."
-echo "Output files:"
+    mkdir -p \$(dirname "\$output_location") && echo "Containing directory \$output_location created"
-echo "par_output:"
-ls "\$par_output"
 
-echo
+    echo "Copying files..."
-echo "par_output_falco:"
+    cp -rL "\$input_location" "\$output_location"
-ls "\$par_output_falco"
 
-echo
+    echo "Output files for \$output_location:"
-echo "par_output_multiqc:"
+    ls "\$output_location"
-ls "\$par_output_multiqc"
+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

target/executable/io/untar/.config.vsh.yaml

@@ -148,9 +148,9 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/executable/io/untar/untar

@@ -476,9 +476,9 @@ 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="2024-12-18T15:00:54Z"
+LABEL org.opencontainers.image.created="2024-12-19T15:39:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="8d3c2888d6df6688763d303dba03ce53d339fb0f"
+LABEL org.opencontainers.image.revision="798e361afeea8dbb84dc23ef38e4fbc3883463e7"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/nextflow/dataflow/combine_samples/.config.vsh.yaml

@@ -139,9 +139,9 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/nextflow/dataflow/combine_samples/main.nf

@@ -2972,9 +2972,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",

target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml

@@ -133,9 +133,9 @@ 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: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -2965,9 +2965,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",

target/nextflow/demultiplex/.config.vsh.yaml

@@ -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: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"

target/nextflow/demultiplex/main.nf

@@ -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" : ";"
         }
       ]
     }
@@ -3088,9 +3101,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -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",
         ]
       )
 

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"
+            }
+    
+
 }
 },
     

target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml

@@ -141,9 +141,9 @@ 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: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -2977,9 +2977,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",

target/nextflow/io/publish/.config.vsh.yaml

@@ -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"
@@ -170,9 +191,9 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/nextflow/io/publish/main.nf

@@ -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" : ";"
         }
       ]
     }
@@ -3012,9 +3036,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -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"
+set -eo pipefail
-echo "Publishing \\$par_input_falco -> \\$par_output_falco"
-echo "Publishing \\$par_input_multiqc -> \\$par_output_multiqc"
 
-echo
+declare -A input_output_mapping=(["par_input"]="par_output" 
-echo "Creating directory if it does not exist:"
+                                 ["par_input_falco"]="par_output_falco" 
-mkdir -p \\$(dirname "\\$par_output") && echo "Containing directory \\$par_output created"
+                                 ["par_input_multiqc"]="par_output_multiqc"
-mkdir -p \\$(dirname "\\$par_output_falco") && echo "Containing directory \\$par_output_falco created"
+                                 ["par_input_run_information"]="par_output_run_information"
-mkdir -p \\$(dirname "\\$par_output_multiqc") && echo "Containing directory \\$par_output_multiqc created"
+                                )
 
-echo
+for input_argument_name in "\\${!input_output_mapping[@]}"
-echo "Copying files..."
+do
-cp -rL "\\$par_input" "\\$par_output"
+    input_location="\\${!input_argument_name}"
-cp -rL "\\$par_input_falco" "\\$par_output_falco"
+    output_argument_name="\\${input_output_mapping[\\$input_argument_name]}"
-cp -rL "\\$par_input_multiqc" "\\$par_output_multiqc"
+    output_location="\\${!output_argument_name}"
+    echo "Publishing \\$input_location -> \\$output_location"
 
-echo
+    echo "Creating directory if it does not exist."
-echo "Output files:"
+    mkdir -p \\$(dirname "\\$output_location") && echo "Containing directory \\$output_location created"
-echo "par_output:"
-ls "\\$par_output"
 
-echo
+    echo "Copying files..."
-echo "par_output_falco:"
+    cp -rL "\\$input_location" "\\$output_location"
-ls "\\$par_output_falco"
 
-echo
+    echo "Output files for \\$output_location:"
-echo "par_output_multiqc:"
+    ls "\\$output_location"
-ls "\\$par_output_multiqc"
+done
 VIASHMAIN
 bash "$tempscript"
 '''

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",
+                "description": "Type: `file`, required. Location where to write the MultiQC report to",
-                "help_text": "Type: `file`, required. Directory to write falco output 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"
+            }
+    
+
 }
 },
     

target/nextflow/io/untar/.config.vsh.yaml

@@ -148,9 +148,9 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
   name: "demultiplex"
   version: "main"

target/nextflow/io/untar/main.nf

@@ -2989,9 +2989,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",

target/nextflow/runner/.config.vsh.yaml

@@ -179,9 +179,9 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_tag: "v0.1.1-13-g798e361"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"

target/nextflow/runner/main.nf

@@ -3021,9 +3021,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.0",
-    "git_commit" : "8d3c2888d6df6688763d303dba03ce53d339fb0f",
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_tag" : "v0.1.1-13-g798e361"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3090,14 +3090,20 @@ workflow run_wf {
         ]
       }
       | demultiplex.run(
-        fromState: [
+        fromState: { id, state ->
-          "input": "input",
+          def state_to_pass = [
-          "run_information": "run_information",
+            "input": state.input,
-          "demultiplexer": "demultiplexer",
+            "run_information": state.run_information,
-          "output": "fastq",
+            "demultiplexer": state.demultiplexer,
-          "output_falco": "qc/fastqc",
+            "output": "fastq",
-          "output_multiqc": "qc/multiqc_report.html"
+            "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
         },
@@ -3111,6 +3117,7 @@ workflow run_wf {
           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 (id2 == "run") {
             println("Publising to ${params.publish_dir}")
@@ -3122,9 +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 -> [:] },