Build branch move-detect-demultiplex-subworkflow with version move-detect-demultiplex-subworkflow (f772bbb)

Build pipeline: viash-hub.demultiplex.move-detect-demultiplex-subworkflow-npp4p Source commit: f772bbb914 Source message: trigger ci
2025-06-05 13:16:24 +00:00
parent 775f457aff
commit 17574aa735
25 changed files with 67 additions and 59 deletions
--- a/src/detect_demultiplexer/config.vsh.yaml
+++ b/src/detect_demultiplexer/config.vsh.yaml
@@ -1,7 +1,7 @@
 name: detect_demultiplexer
 description: |
-  Detects the demultiplexer used to generate the fastq files and runs the appropriate
-  demultiplexing workflow.
+  Detects the demultiplexer and accompanying sample information file which can be 
+  used to generate the fastq files.
 arguments:
  - name: --id
    description: Unique identifier for the run
@@ -30,12 +30,17 @@ arguments:
      required.

  - name: --demultiplexer_output
-    description: Output demultiplexer
+    description: |
+      Demultiplexer program. The demultiplexer is either provided (with --demultiplexer), 
+      or inferred from the contents of the input data.
    type: string
    direction: output
    required: false
  - name: --run_information_output
-    description: Output run information
+    description: |
+      Sample information that can be used to demultiplex the input data. 
+      An appropriate file was either provided (with --run_information), or 
+      inferred from the contents of the input data.
    type: file
    direction: output
    required: false
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -157,9 +157,9 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -454,9 +454,9 @@ 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="2025-05-27T14:23:50Z"
+LABEL org.opencontainers.image.created="2025-06-05T12:20:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="84bb47bfb87cd0420f52ec97c15236311de4c94c"
+LABEL org.opencontainers.image.revision="f772bbb9140df60416f526b6031456492dc025a1"
 LABEL org.opencontainers.image.version="move-detect-demultiplex-subworkflow"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -219,9 +219,9 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -450,9 +450,9 @@ 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="2025-05-27T14:23:50Z"
+LABEL org.opencontainers.image.created="2025-06-05T12:20:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="84bb47bfb87cd0420f52ec97c15236311de4c94c"
+LABEL org.opencontainers.image.revision="f772bbb9140df60416f526b6031456492dc025a1"
 LABEL org.opencontainers.image.version="move-detect-demultiplex-subworkflow"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -450,9 +450,9 @@ 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="2025-05-27T14:23:50Z"
+LABEL org.opencontainers.image.created="2025-06-05T12:20:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="84bb47bfb87cd0420f52ec97c15236311de4c94c"
+LABEL org.opencontainers.image.revision="f772bbb9140df60416f526b6031456492dc025a1"
 LABEL org.opencontainers.image.version="move-detect-demultiplex-subworkflow"

 VIASHDOCKER
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -165,9 +165,9 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -3230,9 +3230,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "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
@@ -156,9 +156,9 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -3227,9 +3227,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -261,9 +261,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3369,9 +3369,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml
+++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
@@ -49,7 +49,8 @@ argument_groups:
    multiple_sep: ";"
  - type: "string"
    name: "--demultiplexer_output"
-    description: "Output demultiplexer"
+    description: "Demultiplexer program. The demultiplexer is either provided (with\
+      \ --demultiplexer), \nor inferred from the contents of the input data.\n"
    info: null
    required: false
    direction: "output"
@@ -57,7 +58,9 @@ argument_groups:
    multiple_sep: ";"
  - type: "file"
    name: "--run_information_output"
-    description: "Output run information"
+    description: "Sample information that can be used to demultiplex the input data.\
+      \ \nAn appropriate file was either provided (with --run_information), or \n\
+      inferred from the contents of the input data.\n"
    info: null
    must_exist: true
    create_parent: true
@@ -73,8 +76,8 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
-description: "Detects the demultiplexer used to generate the fastq files and runs\
-  \ the appropriate\ndemultiplexing workflow.\n"
+description: "Detects the demultiplexer and accompanying sample information file which\
+  \ can be \nused to generate the fastq files.\n"
 info: null
 status: "enabled"
 scope:
@@ -162,9 +165,9 @@ build_info:
  output: "target/nextflow/detect_demultiplexer"
  executable: "target/nextflow/detect_demultiplexer/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -3083,7 +3083,7 @@ meta = [
        {
          "type" : "string",
          "name" : "--demultiplexer_output",
-          "description" : "Output demultiplexer",
+          "description" : "Demultiplexer program. The demultiplexer is either provided (with --demultiplexer), \nor inferred from the contents of the input data.\n",
          "required" : false,
          "direction" : "output",
          "multiple" : false,
@@ -3092,7 +3092,7 @@ meta = [
        {
          "type" : "file",
          "name" : "--run_information_output",
-          "description" : "Output run information",
+          "description" : "Sample information that can be used to demultiplex the input data. \nAn appropriate file was either provided (with --run_information), or \ninferred from the contents of the input data.\n",
          "must_exist" : true,
          "create_parent" : true,
          "required" : false,
@@ -3116,7 +3116,7 @@ meta = [
      "dest" : "nextflow_labels.config"
    }
  ],
-  "description" : "Detects the demultiplexer used to generate the fastq files and runs the appropriate\ndemultiplexing workflow.\n",
+  "description" : "Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n",
  "status" : "enabled",
  "scope" : {
    "image" : "public",
@@ -3219,9 +3219,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/detect_demultiplexer",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/detect_demultiplexer/nextflow.config
+++ b/target/nextflow/detect_demultiplexer/nextflow.config
@@ -3,7 +3,7 @@ manifest {
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
  version = 'move-detect-demultiplex-subworkflow'
-  description = 'Detects the demultiplexer used to generate the fastq files and runs the appropriate\ndemultiplexing workflow.\n'
+  description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/nextflow/detect_demultiplexer/nextflow_schema.json
+++ b/target/nextflow/detect_demultiplexer/nextflow_schema.json
@@ -1,7 +1,7 @@
 {
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "detect_demultiplexer",
-  "description": "Detects the demultiplexer used to generate the fastq files and runs the appropriate\ndemultiplexing workflow.\n",
+  "description": "Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n",
  "type": "object",
  "$defs": {
    "arguments": {
@@ -38,13 +38,13 @@
        },
        "demultiplexer_output": {
          "type": "string",
-          "description": "Output demultiplexer",
+          "description": "Demultiplexer program",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "run_information_output": {
          "type": "string",
          "format": "path",
-          "description": "Output run information",
+          "description": "Sample information that can be used to demultiplex the input data",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_information_output\"`, direction: `output`. ",
          "default": "$id.$key.run_information_output"
        }
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -157,9 +157,9 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -3228,9 +3228,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -219,9 +219,9 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3297,9 +3297,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
 package_config:
  name: "demultiplex"
  version: "move-detect-demultiplex-subworkflow"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -3227,9 +3227,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -206,9 +206,9 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.4"
-  git_commit: "84bb47bfb87cd0420f52ec97c15236311de4c94c"
+  git_commit: "f772bbb9140df60416f526b6031456492dc025a1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-31-g84bb47b"
+  git_tag: "v0.1.1-34-gf772bbb"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3283,9 +3283,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "84bb47bfb87cd0420f52ec97c15236311de4c94c",
+    "git_commit" : "f772bbb9140df60416f526b6031456492dc025a1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-31-g84bb47b"
+    "git_tag" : "v0.1.1-34-gf772bbb"
  },
  "package_config" : {
    "name" : "demultiplex",