Build branch check-resources with version check-resources (cfc11db)

Build pipeline: viash-hub.toolbox.check-resources-cxbsm

Source commit: cfc11db17d

Source message: add changelog entry

target/executable/bgzip/.config.vsh.yaml

@@ -0,0 +1,267 @@
+name: "bgzip"
+version: "check-resources"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "file to be compressed or decompressed"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "compressed or decompressed output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index_name"
+    alternatives:
+    - "-I"
+    description: "name of BGZF index file [file.gz.gzi]"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "integer"
+    name: "--offset"
+    alternatives:
+    - "-b"
+    description: "decompress at virtual file pointer (0-based uncompressed offset)"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--decompress"
+    alternatives:
+    - "-d"
+    description: "decompress the input file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rebgzip"
+    alternatives:
+    - "-g"
+    description: "use an index file to bgzip a file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--index"
+    alternatives:
+    - "-i"
+    description: "compress and create BGZF index"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--compress_level"
+    alternatives:
+    - "-l"
+    description: "compression level to use when compressing; 0 to 9, or -1 for default\
+      \ [-1]"
+    info: null
+    required: false
+    min: -1
+    max: 9
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--reindex"
+    alternatives:
+    - "-r"
+    description: "(re)index the output file"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--size"
+    alternatives:
+    - "-s"
+    description: "decompress INT bytes (uncompressed size)"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--test"
+    alternatives:
+    - "-t"
+    description: "test integrity of compressed file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--binary"
+    description: "Don't align blocks with text lines"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Block compression/decompression utility"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/gigascience/giab007"
+links:
+  repository: "https://github.com/samtools/htslib"
+  homepage: "https://www.htslib.org/"
+  documentation: "https://www.htslib.org/doc/bgzip.html"
+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: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "check-resources"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\\s\\(.*\\)/bgzip: \"\\1\"\
+      /' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bgzip/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bgzip"
+  executable: "target/executable/bgzip/bgzip"
+  viash_version: "0.9.4"
+  git_commit: "cfc11db17dde3001289ba6d31c1172dbee58091b"
+  git_remote: "https://github.com/viash-hub/toolbox"
+package_config:
+  name: "toolbox"
+  version: "check-resources"
+  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 := 'check-resources'"
+  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"