Build branch main with version main (0e87de8)

Build pipeline: viash-hub.htrnaseq.main-29nvl

Source commit: 0e87de80bc

Source message: Bump craftbox to v0.2.0 (#62)

CHANGELOG.md

@@ -1,3 +1,15 @@
+# htrnaseq v0.8.3
+
+## Minor changes
+
+* Bump craftbox to v0.2.0 (PR #62).
+
+# htrnaseq v0.8.2
+
+## Under the hood
+
+* Add the package config (`_viash.yaml`) to every component's target dir. This makes introspection from, e.g. a `runner` workflow much more robust (PR #61)
+
 # htrnaseq v0.8.1
 
 ## Bug fixes

_viash.yaml

@@ -52,3 +52,5 @@ config_mods: |
   .requirements.commands := ['ps']
   .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
   .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+

src/utils/concatRuns/config.vsh.yaml

@@ -35,7 +35,7 @@ repositories:
   - name: cb
     type: vsh
     repo: craftbox
-    tag: v0.1.0
+    tag: v0.2.0
 runners:
   - type: nextflow
 

src/workflows/runner/main.nf

@@ -1,6 +1,6 @@
 def date = new Date().format('yyyyMMdd_hhmmss')
 
-def viash_config = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
+def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
 workflow run_wf {

target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text/.config.vsh.yaml

@@ -1,197 +0,0 @@
-name: "concat_text"
-version: "v0.1.0"
-authors:
-- name: "Toni Verbeiren"
-  roles:
-  - "author"
-  - "maintainer"
-  info:
-    links:
-      github: "tverbeiren"
-      linkedin: "verbeiren"
-    organizations:
-    - name: "Data Intuitive"
-      href: "https://www.data-intuitive.com"
-      role: "Data Scientist and CEO"
-- name: "Dries Schaumont"
-  roles:
-  - "reviewer"
-  info:
-    links:
-      email: "dries@data-intuitive.com"
-      github: "DriesSchaumont"
-      orcid: "0000-0002-4389-0440"
-      linkedin: "dries-schaumont"
-    organizations:
-    - name: "Data Intuitive"
-      href: "https://www.data-intuitive.com"
-      role: "Data Scientist"
-argument_groups:
-- name: "Input arguments"
-  arguments:
-  - type: "file"
-    name: "--input"
-    description: "A list of (gzipped) text files."
-    info: null
-    example:
-    - "input?.txt.gz"
-    must_exist: true
-    create_parent: true
-    required: true
-    direction: "input"
-    multiple: true
-    multiple_sep: ";"
-- name: "Output arguments"
-  arguments:
-  - type: "boolean_true"
-    name: "--gzip_output"
-    description: "Should the output be zipped?"
-    info: null
-    direction: "input"
-  - type: "file"
-    name: "--output"
-    description: "File to write the output to, optionally gzipped."
-    info: null
-    example:
-    - "output.txt"
-    must_exist: true
-    create_parent: true
-    required: false
-    direction: "output"
-    multiple: false
-    multiple_sep: ";"
-resources:
-- type: "bash_script"
-  path: "script.sh"
-  is_executable: true
-description: "Concatenate a number of text files, handle gzipped text files gracefully\
-  \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
-  \ fastq files from different lanes, for instance.\n"
-test_resources:
-- type: "bash_script"
-  path: "test.sh"
-  is_executable: true
-info:
-  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
-    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
-    \ for the output\n"
-status: "enabled"
-requirements:
-  commands:
-  - "ps"
-license: "MIT"
-links:
-  repository: "https://github.com/viash-hub/craftbox"
-runners:
-- type: "executable"
-  id: "executable"
-  docker_setup_strategy: "ifneedbepullelsecachedbuild"
-- type: "nextflow"
-  id: "nextflow"
-  directives:
-    tag: "$id"
-  auto:
-    simplifyInput: true
-    simplifyOutput: false
-    transcript: false
-    publish: false
-  config:
-    labels:
-      mem1gb: "memory = 1000000000.B"
-      mem2gb: "memory = 2000000000.B"
-      mem5gb: "memory = 5000000000.B"
-      mem10gb: "memory = 10000000000.B"
-      mem20gb: "memory = 20000000000.B"
-      mem50gb: "memory = 50000000000.B"
-      mem100gb: "memory = 100000000000.B"
-      mem200gb: "memory = 200000000000.B"
-      mem500gb: "memory = 500000000000.B"
-      mem1tb: "memory = 1000000000000.B"
-      mem2tb: "memory = 2000000000000.B"
-      mem5tb: "memory = 5000000000000.B"
-      mem10tb: "memory = 10000000000000.B"
-      mem20tb: "memory = 20000000000000.B"
-      mem50tb: "memory = 50000000000000.B"
-      mem100tb: "memory = 100000000000000.B"
-      mem200tb: "memory = 200000000000000.B"
-      mem500tb: "memory = 500000000000000.B"
-      mem1gib: "memory = 1073741824.B"
-      mem2gib: "memory = 2147483648.B"
-      mem4gib: "memory = 4294967296.B"
-      mem8gib: "memory = 8589934592.B"
-      mem16gib: "memory = 17179869184.B"
-      mem32gib: "memory = 34359738368.B"
-      mem64gib: "memory = 68719476736.B"
-      mem128gib: "memory = 137438953472.B"
-      mem256gib: "memory = 274877906944.B"
-      mem512gib: "memory = 549755813888.B"
-      mem1tib: "memory = 1099511627776.B"
-      mem2tib: "memory = 2199023255552.B"
-      mem4tib: "memory = 4398046511104.B"
-      mem8tib: "memory = 8796093022208.B"
-      mem16tib: "memory = 17592186044416.B"
-      mem32tib: "memory = 35184372088832.B"
-      mem64tib: "memory = 70368744177664.B"
-      mem128tib: "memory = 140737488355328.B"
-      mem256tib: "memory = 281474976710656.B"
-      mem512tib: "memory = 562949953421312.B"
-      cpu1: "cpus = 1"
-      cpu2: "cpus = 2"
-      cpu5: "cpus = 5"
-      cpu10: "cpus = 10"
-      cpu20: "cpus = 20"
-      cpu50: "cpus = 50"
-      cpu100: "cpus = 100"
-      cpu200: "cpus = 200"
-      cpu500: "cpus = 500"
-      cpu1000: "cpus = 1000"
-  debug: false
-  container: "docker"
-engines:
-- type: "docker"
-  id: "docker"
-  image: "alpine:latest"
-  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
-  namespace_separator: "/"
-  setup:
-  - type: "apk"
-    packages:
-    - "bash"
-    - "procps"
-    - "file"
-  entrypoint: []
-  cmd: null
-- type: "native"
-  id: "native"
-build_info:
-  config: "src/concat_text/config.vsh.yaml"
-  runner: "nextflow"
-  engine: "docker|native"
-  output: "target/nextflow/concat_text"
-  executable: "target/nextflow/concat_text/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
-  git_remote: "https://github.com/viash-hub/craftbox"
-package_config:
-  name: "craftbox"
-  version: "v0.1.0"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
-  info: null
-  viash_version: "0.9.0"
-  source: "src"
-  target: "target"
-  config_mods:
-  - ".requirements.commands := ['ps']\n"
-  - ".engines += { type: \"native\" }"
-  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
-  keywords:
-  - "scripts"
-  - "custom"
-  - "implementations"
-  license: "MIT"
-  organization: "vsh"
-  links:
-    repository: "https://github.com/viash-hub/craftbox"
-    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text/nextflow.config

@@ -1,126 +0,0 @@
-manifest {
-  name = 'concat_text'
-  mainScript = 'main.nf'
-  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
-  description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
-  author = 'Toni Verbeiren, Dries Schaumont'
-}
-
-process.container = 'nextflow/bash:latest'
-
-// detect tempdir
-tempDir = java.nio.file.Paths.get(
-  System.getenv('NXF_TEMP') ?:
-    System.getenv('VIASH_TEMP') ?: 
-    System.getenv('TEMPDIR') ?: 
-    System.getenv('TMPDIR') ?: 
-    '/tmp'
-).toAbsolutePath()
-
-profiles {
-  no_publish {
-    process {
-      withName: '.*' {
-        publishDir = [
-          enabled: false
-        ]
-      }
-    }
-  }
-  mount_temp {
-    docker.temp            = tempDir
-    podman.temp            = tempDir
-    charliecloud.temp      = tempDir
-  }
-  docker {
-    docker.enabled         = true
-    // docker.userEmulation   = true
-    singularity.enabled    = false
-    podman.enabled         = false
-    shifter.enabled        = false
-    charliecloud.enabled   = false
-  }
-  singularity {
-    singularity.enabled    = true
-    singularity.autoMounts = true
-    docker.enabled         = false
-    podman.enabled         = false
-    shifter.enabled        = false
-    charliecloud.enabled   = false
-  }
-  podman {
-    podman.enabled         = true
-    docker.enabled         = false
-    singularity.enabled    = false
-    shifter.enabled        = false
-    charliecloud.enabled   = false
-  }
-  shifter {
-    shifter.enabled        = true
-    docker.enabled         = false
-    singularity.enabled    = false
-    podman.enabled         = false
-    charliecloud.enabled   = false
-  }
-  charliecloud {
-    charliecloud.enabled   = true
-    docker.enabled         = false
-    singularity.enabled    = false
-    podman.enabled         = false
-    shifter.enabled        = false
-  }
-}
-
-process{
-  withLabel: mem1gb { memory = 1000000000.B }
-  withLabel: mem2gb { memory = 2000000000.B }
-  withLabel: mem5gb { memory = 5000000000.B }
-  withLabel: mem10gb { memory = 10000000000.B }
-  withLabel: mem20gb { memory = 20000000000.B }
-  withLabel: mem50gb { memory = 50000000000.B }
-  withLabel: mem100gb { memory = 100000000000.B }
-  withLabel: mem200gb { memory = 200000000000.B }
-  withLabel: mem500gb { memory = 500000000000.B }
-  withLabel: mem1tb { memory = 1000000000000.B }
-  withLabel: mem2tb { memory = 2000000000000.B }
-  withLabel: mem5tb { memory = 5000000000000.B }
-  withLabel: mem10tb { memory = 10000000000000.B }
-  withLabel: mem20tb { memory = 20000000000000.B }
-  withLabel: mem50tb { memory = 50000000000000.B }
-  withLabel: mem100tb { memory = 100000000000000.B }
-  withLabel: mem200tb { memory = 200000000000000.B }
-  withLabel: mem500tb { memory = 500000000000000.B }
-  withLabel: mem1gib { memory = 1073741824.B }
-  withLabel: mem2gib { memory = 2147483648.B }
-  withLabel: mem4gib { memory = 4294967296.B }
-  withLabel: mem8gib { memory = 8589934592.B }
-  withLabel: mem16gib { memory = 17179869184.B }
-  withLabel: mem32gib { memory = 34359738368.B }
-  withLabel: mem64gib { memory = 68719476736.B }
-  withLabel: mem128gib { memory = 137438953472.B }
-  withLabel: mem256gib { memory = 274877906944.B }
-  withLabel: mem512gib { memory = 549755813888.B }
-  withLabel: mem1tib { memory = 1099511627776.B }
-  withLabel: mem2tib { memory = 2199023255552.B }
-  withLabel: mem4tib { memory = 4398046511104.B }
-  withLabel: mem8tib { memory = 8796093022208.B }
-  withLabel: mem16tib { memory = 17592186044416.B }
-  withLabel: mem32tib { memory = 35184372088832.B }
-  withLabel: mem64tib { memory = 70368744177664.B }
-  withLabel: mem128tib { memory = 140737488355328.B }
-  withLabel: mem256tib { memory = 281474976710656.B }
-  withLabel: mem512tib { memory = 562949953421312.B }
-  withLabel: cpu1 { cpus = 1 }
-  withLabel: cpu2 { cpus = 2 }
-  withLabel: cpu5 { cpus = 5 }
-  withLabel: cpu10 { cpus = 10 }
-  withLabel: cpu20 { cpus = 20 }
-  withLabel: cpu50 { cpus = 50 }
-  withLabel: cpu100 { cpus = 100 }
-  withLabel: cpu200 { cpus = 200 }
-  withLabel: cpu500 { cpus = 500 }
-  withLabel: cpu1000 { cpus = 1000 }
-}
-
-

target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text/nextflow_schema.json

@@ -1,106 +0,0 @@
-{
-"$schema": "http://json-schema.org/draft-07/schema",
-"title": "concat_text",
-"description": "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
-"type": "object",
-"definitions": {
-
-    
-    
-    "input arguments" : {
-    "title": "Input arguments",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "input": {
-                "type":
-                "string",
-                "description": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files",
-                "help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files."
-            
-            }
-    
-
-}
-},
-    
-    
-    "output arguments" : {
-    "title": "Output arguments",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "gzip_output": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Should the output be zipped?",
-                "help_text": "Type: `boolean_true`, default: `false`. Should the output be zipped?"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "output": {
-                "type":
-                "string",
-                "description": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped",
-                "help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped."
-            ,
-                "default": "$id.$key.output.txt"
-            }
-    
-
-}
-},
-    
-    
-    "nextflow input-output arguments" : {
-    "title": "Nextflow input-output arguments",
-    "type": "object",
-    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
-    "properties": {
-    
-        
-                "publish_dir": {
-                "type":
-                "string",
-                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
-                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
-            
-            }
-    
-
-        ,
-                "param_list": {
-                "type":
-                "string",
-                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
-                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
-                "hidden": true
-            
-            }
-    
-
-}
-}
-},
-"allOf": [
-
-    {
-    "$ref": "#/definitions/input arguments"
-    },
-
-    {
-    "$ref": "#/definitions/output arguments"
-    },
-
-    {
-    "$ref": "#/definitions/nextflow input-output arguments"
-    }
-]
-}

target/executable/eset/create_eset/.config.vsh.yaml

@@ -82,6 +82,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "r_script"
   path: "test.R"
@@ -203,9 +206,9 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -236,7 +239,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/eset/create_eset/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/eset/create_eset/create_eset

@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/eset/create_fdata/.config.vsh.yaml

@@ -61,6 +61,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Create a fdata file\n"
 test_resources:
 - type: "python_script"
@@ -180,9 +183,9 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -213,7 +216,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/eset/create_fdata/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/eset/create_fdata/create_fdata

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:21Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/eset/create_pdata/.config.vsh.yaml

@@ -73,6 +73,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Create a pdata file by combining the mapping statistics \n"
 test_resources:
 - type: "python_script"
@@ -194,9 +197,9 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -227,7 +230,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/eset/create_pdata/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/eset/create_pdata/create_pdata

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -47,6 +47,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "This component test the ExpressionSet object as output by the main pipeline."
 info: null
 status: "enabled"
@@ -152,9 +155,9 @@ build_info:
   output: "target/executable/integration_test_components/htrnaseq/check_eset"
   executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -185,7 +188,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/integration_test_components/htrnaseq/check_eset/check_eset

@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -54,6 +54,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "This component test the cutadapt output from the well_demultiplex subworkflow."
 info: null
 status: "enabled"
@@ -161,9 +164,9 @@ build_info:
   output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -194,7 +197,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -34,6 +34,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Publish the fastq files per well"
 info: null
 status: "enabled"
@@ -136,9 +139,9 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -169,7 +172,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/io/publish_fastqs/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/io/publish_fastqs/publish_fastqs

@@ -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_fastqs"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -97,6 +97,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Publish the results"
 info: null
 status: "enabled"
@@ -199,9 +202,9 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -232,7 +235,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/io/publish_results/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/io/publish_results/publish_results

@@ -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_results"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:21Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/parallel_map/.config.vsh.yaml

@@ -156,6 +156,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference\
   \ (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n"
 test_resources:
@@ -282,9 +285,9 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -315,7 +318,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/parallel_map/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/parallel_map/parallel_map

@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:23Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/report/create_report/.config.vsh.yaml

@@ -66,6 +66,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Create a basic QC report in HTML format based on a number of esets.\n"
 test_resources:
 - type: "r_script"
@@ -212,9 +215,9 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -245,7 +248,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/report/create_report/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/report/create_report/create_report

@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:21Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/stats/combine_star_logs/.config.vsh.yaml

@@ -83,6 +83,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "python_script"
   path: "test.py"
@@ -201,9 +204,9 @@ build_info:
   output: "target/executable/stats/combine_star_logs"
   executable: "target/executable/stats/combine_star_logs/combine_star_logs"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -234,7 +237,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/stats/combine_star_logs/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/stats/combine_star_logs/combine_star_logs

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:21Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/stats/generate_pool_statistics/.config.vsh.yaml

@@ -69,6 +69,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "python_script"
   path: "test.py"
@@ -185,9 +188,9 @@ build_info:
   output: "target/executable/stats/generate_pool_statistics"
   executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -218,7 +221,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/stats/generate_pool_statistics/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/stats/generate_pool_statistics/generate_pool_statistics

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:20Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/stats/generate_well_statistics/.config.vsh.yaml

@@ -135,6 +135,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Generate summary statistics from BAM files generated by STAR solo."
 test_resources:
 - type: "python_script"
@@ -267,9 +270,9 @@ build_info:
   output: "target/executable/stats/generate_well_statistics"
   executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -300,7 +303,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/stats/generate_well_statistics/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/stats/generate_well_statistics/generate_well_statistics

@@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:21Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/utils/save_params/.config.vsh.yaml

@@ -41,6 +41,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Save parameters to a YAML file\n"
 info: null
 status: "enabled"
@@ -148,9 +151,9 @@ build_info:
   output: "target/executable/utils/save_params"
   executable: "target/executable/utils/save_params/save_params"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -181,7 +184,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/executable/utils/save_params/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/executable/utils/save_params/save_params

@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "pyyaml"
 
 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:21Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/nextflow/eset/create_eset/.config.vsh.yaml

@@ -82,6 +82,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "r_script"
   path: "test.R"
@@ -203,9 +206,9 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -236,7 +239,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/eset/create_eset/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/eset/create_eset/main.nf

@@ -3148,6 +3148,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "test_resources" : [
@@ -3304,9 +3309,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3325,7 +3330,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/eset/create_fdata/.config.vsh.yaml

@@ -61,6 +61,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Create a fdata file\n"
 test_resources:
 - type: "python_script"
@@ -180,9 +183,9 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -213,7 +216,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/eset/create_fdata/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/eset/create_fdata/main.nf

@@ -3122,6 +3122,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Create a fdata file\n",
@@ -3274,9 +3279,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3295,7 +3300,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/eset/create_pdata/.config.vsh.yaml

@@ -73,6 +73,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Create a pdata file by combining the mapping statistics \n"
 test_resources:
 - type: "python_script"
@@ -194,9 +197,9 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -227,7 +230,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/eset/create_pdata/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/eset/create_pdata/main.nf

@@ -3132,6 +3132,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Create a pdata file by combining the mapping statistics \n",
@@ -3288,9 +3293,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3309,7 +3314,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -47,6 +47,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "This component test the ExpressionSet object as output by the main pipeline."
 info: null
 status: "enabled"
@@ -152,9 +155,9 @@ build_info:
   output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
   executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -185,7 +188,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf

@@ -3101,6 +3101,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "This component test the ExpressionSet object as output by the main pipeline.",
@@ -3228,9 +3233,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3249,7 +3254,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -54,6 +54,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "This component test the cutadapt output from the well_demultiplex subworkflow."
 info: null
 status: "enabled"
@@ -161,9 +164,9 @@ build_info:
   output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -194,7 +197,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf

@@ -3108,6 +3108,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "This component test the cutadapt output from the well_demultiplex subworkflow.",
@@ -3239,9 +3244,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3260,7 +3265,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

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

@@ -34,6 +34,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Publish the fastq files per well"
 info: null
 status: "enabled"
@@ -136,9 +139,9 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -169,7 +172,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/io/publish_fastqs/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/io/publish_fastqs/main.nf

@@ -3079,6 +3079,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Publish the fastq files per well",
@@ -3202,9 +3207,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3223,7 +3228,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

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

@@ -97,6 +97,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Publish the results"
 info: null
 status: "enabled"
@@ -199,9 +202,9 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -232,7 +235,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/io/publish_results/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/io/publish_results/main.nf

@@ -3149,6 +3149,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Publish the results",
@@ -3272,9 +3277,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3293,7 +3298,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/parallel_map/.config.vsh.yaml

@@ -156,6 +156,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference\
   \ (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n"
 test_resources:
@@ -282,9 +285,9 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -315,7 +318,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/parallel_map/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/parallel_map/main.nf

@@ -3220,6 +3220,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
@@ -3374,9 +3379,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3395,7 +3400,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/report/create_report/.config.vsh.yaml

@@ -66,6 +66,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Create a basic QC report in HTML format based on a number of esets.\n"
 test_resources:
 - type: "r_script"
@@ -212,9 +215,9 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -245,7 +248,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/report/create_report/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/report/create_report/main.nf

@@ -3135,6 +3135,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Create a basic QC report in HTML format based on a number of esets.\n",
@@ -3318,9 +3323,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3339,7 +3344,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/stats/combine_star_logs/.config.vsh.yaml

@@ -83,6 +83,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "python_script"
   path: "test.py"
@@ -201,9 +204,9 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -234,7 +237,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/stats/combine_star_logs/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/stats/combine_star_logs/main.nf

@@ -3139,6 +3139,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "test_resources" : [
@@ -3290,9 +3295,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3311,7 +3316,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml

@@ -69,6 +69,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "python_script"
   path: "test.py"
@@ -185,9 +188,9 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -218,7 +221,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/stats/generate_pool_statistics/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/stats/generate_pool_statistics/main.nf

@@ -3127,6 +3127,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "test_resources" : [
@@ -3274,9 +3279,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3295,7 +3300,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/stats/generate_well_statistics/.config.vsh.yaml

@@ -135,6 +135,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Generate summary statistics from BAM files generated by STAR solo."
 test_resources:
 - type: "python_script"
@@ -267,9 +270,9 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -300,7 +303,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/stats/generate_well_statistics/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/stats/generate_well_statistics/main.nf

@@ -3199,6 +3199,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Generate summary statistics from BAM files generated by STAR solo.",
@@ -3369,9 +3374,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3390,7 +3395,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/utils/concatRuns/.config.vsh.yaml

@@ -57,6 +57,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Concatenate well FASTQ files from different runs in order to increase\
   \ sequencing depth.\n"
 info: null
@@ -72,12 +75,12 @@ dependencies:
   repository:
     type: "vsh"
     repo: "craftbox"
-    tag: "v0.1.0"
+    tag: "v0.2.0"
 repositories:
 - type: "vsh"
   name: "cb"
   repo: "craftbox"
-  tag: "v0.1.0"
+  tag: "v0.2.0"
 license: "MIT"
 links:
   repository: "https://github.com/viash-hub/htrnaseq"
@@ -157,11 +160,11 @@ build_info:
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
   dependencies:
-  - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
+  - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -192,7 +195,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/utils/concatRuns/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/utils/concatRuns/main.nf

@@ -3101,6 +3101,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n",
@@ -3120,7 +3125,7 @@ meta = [
       "repository" : {
         "type" : "vsh",
         "repo" : "craftbox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
       }
     }
   ],
@@ -3129,7 +3134,7 @@ meta = [
       "type" : "vsh",
       "name" : "cb",
       "repo" : "craftbox",
-      "tag" : "v0.1.0"
+      "tag" : "v0.2.0"
     }
   ],
   "license" : "MIT",
@@ -3224,9 +3229,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3245,7 +3250,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"
@@ -3272,7 +3277,7 @@ meta = [
 
 // resolve dependencies dependencies (if any)
 meta["root_dir"] = getRootDir()
-include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text/main.nf"
+include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf"
 
 // inner workflow
 // user-provided Nextflow code

target/nextflow/utils/listInputDir/.config.vsh.yaml

@@ -80,6 +80,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "List the contents of a directory and parse contained fastq files"
 info: null
 status: "enabled"
@@ -168,9 +171,9 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -201,7 +204,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/utils/listInputDir/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/utils/listInputDir/main.nf

@@ -3129,6 +3129,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "List the contents of a directory and parse contained fastq files",
@@ -3234,9 +3239,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3255,7 +3260,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/utils/save_params/.config.vsh.yaml

@@ -41,6 +41,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Save parameters to a YAML file\n"
 info: null
 status: "enabled"
@@ -148,9 +151,9 @@ build_info:
   output: "target/nextflow/utils/save_params"
   executable: "target/nextflow/utils/save_params/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -181,7 +184,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/utils/save_params/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/utils/save_params/main.nf

@@ -3087,6 +3087,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Save parameters to a YAML file\n",
@@ -3218,9 +3223,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/utils/save_params",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3239,7 +3244,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/workflows/htrnaseq/.config.vsh.yaml

@@ -202,6 +202,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "nextflow_script"
   path: "test.nf"
@@ -342,9 +345,9 @@ build_info:
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
   - "target/nextflow/stats/generate_pool_statistics"
@@ -388,7 +391,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/workflows/htrnaseq/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/workflows/htrnaseq/main.nf

@@ -3275,6 +3275,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "test_resources" : [
@@ -3479,9 +3484,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3500,7 +3505,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"

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

@@ -131,6 +131,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Runner for HT RNA-seq pipeline"
 info: null
 status: "enabled"
@@ -235,9 +238,9 @@ build_info:
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
   dependencies:
   - "target/nextflow/utils/listInputDir"
   - "target/nextflow/workflows/htrnaseq"
@@ -274,7 +277,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/workflows/runner/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/workflows/runner/main.nf

@@ -3194,6 +3194,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Runner for HT RNA-seq pipeline",
@@ -3331,9 +3336,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3352,7 +3357,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
       ".engines[.type == 'docker'].target_tag := 'main'"
@@ -3389,7 +3394,7 @@ include { save_params } from "${meta.resources_dir}/../../../nextflow/utils/save
 // user-provided Nextflow code
 def date = new Date().format('yyyyMMdd_hhmmss')
 
-def viash_config = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
+def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
 workflow run_wf {

target/nextflow/workflows/well_demultiplex/.config.vsh.yaml

@@ -97,6 +97,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Demultiplexing on well level"
 test_resources:
 - type: "nextflow_script"
@@ -214,9 +217,9 @@ build_info:
   output: "target/nextflow/workflows/well_demultiplex"
   executable: "target/nextflow/workflows/well_demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt"
   - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
@@ -250,7 +253,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
   - ".engines[.type == 'docker'].target_tag := 'main'"

target/nextflow/workflows/well_demultiplex/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh