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)
2024-12-19 15:54:37 +00:00
parent 43010e8c57
commit ce3c3eb442
29 changed files with 387 additions and 153 deletions
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/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_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-13-g798e361"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/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_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-13-g798e361"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/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:
+    - "$id/run_information.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "nextflow_script"
  path: "main.nf"
@@ -220,9 +231,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8d3c2888d6df6688763d303dba03ce53d339fb0f"
-  git_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -2900,6 +2900,19 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--output_run_information",
+          "default" : [
+            "$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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "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",
        ]
      )

--- 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
@@ -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_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-13-g798e361"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/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_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/publish/main.nf
+++ b/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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "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"
-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"
 '''
--- 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
@@ -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_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/untar/main.nf
+++ b/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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-13-g798e361"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/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_remote: "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-12-g8d3c288"
+  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-13-g798e361"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/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_remote" : "https://x-access-token:ghs_Iv5SuazXszUy4WWFyKOtFABImrj2oY0GsE3i@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-12-g8d3c288"
+    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
+    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-13-g798e361"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3090,14 +3090,20 @@ workflow run_wf {
        ]
      }
      | demultiplex.run(
-        fromState: [
-          "input": "input",
-          "run_information": "run_information",
-          "demultiplexer": "demultiplexer",
-          "output": "fastq",
-          "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html"
-        ],
+        fromState: { id, state ->
+          def state_to_pass = [
+            "input": state.input,
+            "run_information": state.run_information,
+            "demultiplexer": state.demultiplexer,
+            "output": "fastq",
+            "output_falco": "qc/fastqc",
+            "output_multiqc": "qc/multiqc_report.html",
+          ]
+          if (state.run_information) {
+            state_to_pass += ["output_run_information": state.run_information.getName()] 
+          }
+          state_to_pass
+        },
        toState: { id, result, state ->
          state + result
        },
@@ -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 -> [:] },