toolbox/target/nextflow/yq/.config.vsh.yaml

name: "yq"
version: "main"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "files to be processed"
    info: null
    example:
    - "input.yaml"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "output file"
    info: null
    example:
    - "output.yaml"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Arguments"
  arguments:
  - type: "string"
    name: "--eval"
    description: "expression to evaluate"
    info: null
    example:
    - ".name = \"foo\""
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--indent"
    alternatives:
    - "-I"
    description: "sets indent level for output (default 2)"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--input_format"
    alternatives:
    - "-p"
    description: "parse format for input. (default \"auto\")"
    info: null
    required: false
    choices:
    - "auto"
    - "a"
    - "yaml"
    - "y"
    - "json"
    - "j"
    - "props"
    - "p"
    - "csv"
    - "c"
    - "tsv"
    - "t"
    - "xml"
    - "x"
    - "base64"
    - "uri"
    - "toml"
    - "shell"
    - "s"
    - "lua"
    - "l"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_format"
    alternatives:
    - "-o"
    description: "output format type. (default \"auto\")"
    info: null
    required: false
    choices:
    - "auto"
    - "a"
    - "yaml"
    - "y"
    - "json"
    - "j"
    - "props"
    - "p"
    - "csv"
    - "c"
    - "tsv"
    - "t"
    - "xml"
    - "x"
    - "base64"
    - "uri"
    - "toml"
    - "shell"
    - "s"
    - "lua"
    - "l"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--pretty_print"
    alternatives:
    - "-P"
    description: "pretty print, shorthand for '... style = \"\"'"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  text: |
    #!/bin/sh
    [[ "$par_pretty_print" == "false" ]] && unset par_pretty_print
    yq eval \
      ${par_indent:+-I "${par_indent}"} \
      ${par_input_format:+-p "${par_input_format}"} \
      ${par_output_format:+-o "${par_output_format}"} \
      ${par_pretty_print:+-P} \
      --expression "$par_eval" \
      --no-colors \
      "$par_input" > "$par_output"
    

  dest: "./script.sh"
  is_executable: true
description: "A portable YAML, JSON, XML, CSV, TOML and properties processor"
test_resources:
- type: "bash_script"
  text: "set -e\necho \"name: 'bar'\" > test.yaml\n\"$meta_executable\" --input test.yaml\
    \ --output output.yaml --eval '.name = \"foo\"'\n\"$meta_executable\" --input\
    \ output.yaml --output output2.yaml --eval '.name'\ngrep \"^foo$\" output2.yaml\n"
  dest: "./script.sh"
  is_executable: true
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "ps"
keywords:
- "yaml"
- "json"
- "xml"
- "csv"
- "toml"
- "properties"
license: "MIT"
links:
  repository: "https://github.com/mikefarah/yq"
  homepage: "https://mikefarah.gitbook.io/yq"
  documentation: "https://mikefarah.gitbook.io/yq/"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
  id: "nextflow"
  directives:
    tag: "$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: "main"
  namespace_separator: "/"
  setup:
  - type: "apk"
    packages:
    - "bash"
    - "yq-go"
  - type: "docker"
    run:
    - "/usr/bin/yq --version | sed 's/.*version\\sv\\(.*\\)/yq: \"\\1\"/' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/yq/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/yq"
  executable: "target/nextflow/yq/main.nf"
  viash_version: "0.9.4"
  git_commit: "69c4536b849c9a776972a12162376f824b4b4504"
  git_remote: "https://github.com/viash-hub/toolbox"
package_config:
  name: "toolbox"
  version: "main"
  summary: "A collection of curated command-line tools for general IT tasks, built\
    \ with Viash.\n"
  description: "`toolbox` provides a versatile suite of IT components, following the\
    \ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
    \ reliable, standalone tools that can be easily integrated into larger computational\
    \ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
    \ and adherence to **best practices** in component creation. Key features of `toolbox`\
    \ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
    \ directly from the command line or seamlessly incorporate them into Nextflow\
    \ workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
    \ for each component and its parameters.\n    * Full exposure of the underlying\
    \ tool's arguments for maximum flexibility.\n    * Containerized (Docker) to ensure\
    \ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
    \    * Unit tested to verify functionality and ensure reliability.\n"
  info: null
  viash_version: "0.9.4"
  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 := 'main'"
  keywords:
  - "toolbox"
  - "command-line"
  - "tools"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/toolbox"
    issue_tracker: "https://github.com/viash-hub/toolbox/issues"