name: "bgzip"
version: "seqtk_sample"
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"
  text: |
    [[ "$par_decompress" == "false" ]] && unset par_decompress
    [[ "$par_rebgzip" == "false" ]] && unset par_rebgzip
    [[ "$par_index" == "false" ]] && unset par_index
    [[ "$par_reindex" == "false" ]] && unset par_reindex
    [[ "$par_test" == "false" ]] && unset par_test
    [[ "$par_binary" == "false" ]] && unset par_binary
    bgzip -c \
      ${meta_cpus:+--threads "${meta_cpus}"} \
      ${par_offset:+-b "${par_offset}"} \
      ${par_decompress:+-d} \
      ${par_rebgzip:+-g} \
      ${par_index:+-i} \
      ${par_index_name:+-I "${par_index_name}"} \
      ${par_compress_level:+-l "${par_compress_level}"} \
      ${par_reindex:+-r} \
      ${par_size:+-s "${par_size}"} \
      ${par_test:+-t} \
      ${par_binary:+--binary} \
      "$par_input" > "$par_output"
    

  dest: "./script.sh"
  is_executable: true
description: "Block compression/decompression utility"
test_resources:
- type: "bash_script"
  text: "set -e\n\n\"$meta_executable\" --input \"$meta_resources_dir/test_data/test.vcf\"\
    \ --output \"test.vcf.gz\"\n\necho \">> Checking output of compressing\"\n[ !\
    \ -f \"test.vcf.gz\" ] && echo \"Output file test.vcf.gz does not exist\" && exit\
    \ 1\n\n\"$meta_executable\" --input \"test.vcf.gz\" --output \"test.vcf\" --decompress\n\
    \necho \">> Checking output of decompressing\"\n[ ! -f \"test.vcf\" ] && echo\
    \ \"Output file test.vcf does not exist\" && exit 1\n\necho \">> Checking original\
    \ and decompressed files are the same\"\nset +e\ncmp --silent -- \"$meta_resources_dir/test_data/test.vcf\"\
    \ \"test.vcf\"\n[ $? -ne 0 ] && echo \"files are different\" && exit 1\nset -e\n\
    \necho \"> Test successful\"\n"
  dest: "./script.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
license: "MIT"
references:
  doi:
  - "10.1093/gigascience/giab007"
links:
  repository: "https://github.com/samtools/htslib"
  homepage: "https://www.htslib.org/"
  documentation: "https://www.htslib.org/doc/bgzip.html"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
  id: "nextflow"
  directives:
    tag: "$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: "seqtk_sample"
  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: "0.9.0-RC6"
  git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
  git_remote: "https://github.com/viash-hub/biobox"
package_config:
  name: "biobox"
  version: "seqtk_sample"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0-RC6"
  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 := 'seqtk_sample'"
  keywords:
  - "bioinformatics"
  - "sequence"
  - "alignment"
  - "variant calling"
  - "dna"
  - "rna"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/biobbox"
    issue_tracker: "https://github.com/viash-hub/biobox/issues"
