name: "umi_tools_prepareforrsem"
namespace: "umi_tools"
version: "add_sgdemux"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--input"
    alternatives:
    - "-I"
    - "--stdin"
    info: null
    example:
    - "$id.transcriptome.bam"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-S"
    - "--stdout"
    info: null
    example:
    - "$id.transcriptome_sorted.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--log"
    alternatives:
    - "-L"
    description: "File with logging information [default = stdout]."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--error"
    alternatives:
    - "-E"
    description: "File with error information [default = stderr]."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--log2stderr"
    description: "Send logging information to stderr [default = False]."
    info: null
    direction: "input"
  - type: "string"
    name: "--temp_dir"
    description: "Directory for temporary files. If not set, the bash environmental\
      \ variable \nTMPDIR is used.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--compresslevel"
    description: "Level of Gzip compression to use. Default (6) matchesGNU gzip rather\
      \ than python \ngzip default (which is 9).\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "string"
    name: "--tags"
    description: "Comma-seperated list of tags to transfer from read1 to read2 (Default:\
      \ 'UG,BX')\n"
    info: null
    example:
    - "UG,BX"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--sam"
    description: "Input and output SAM rather than BAM."
    info: null
    direction: "input"
  - type: "string"
    name: "--timeit"
    description: "Store timeing information in file [none].\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--timeit_name"
    description: "Name in timing file for this class of jobs [all].\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--timeit_header"
    description: "Add header for timing information [none]."
    info: null
    direction: "input"
  - type: "integer"
    name: "--verbose"
    alternatives:
    - "-v"
    description: "Loglevel [1]. The higher, the more output.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--random_seed"
    description: "Random seed to initialize number generator with [none].\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
- type: "file"
  path: "prepare-for-rsem.py"
description: "Make the output from umi-tools dedup or group compatible with RSEM"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "umi_tools"
- "rsem"
- "bam"
- "sam"
license: "MIT"
references:
  doi:
  - "10.1101/gr.209601.116"
links:
  repository: "https://github.com/CGATOxford/UMI-tools"
  homepage: "https://umi-tools.readthedocs.io/en/latest/"
  documentation: "https://umi-tools.readthedocs.io/en/latest/reference/extract.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/umi_tools:1.1.5--py38h0020b31_3"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "umi_tools -v | sed 's/ version//g' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/umi_tools/umi_tools_prepareforrsem/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/umi_tools/umi_tools_prepareforrsem"
  executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem"
  viash_version: "0.9.0"
  git_commit: "402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
  git_remote: "https://x-access-token:ghs_VWGBwCOTHxXRJ07uVE94xFn8UJ2FmS0FLhmc@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g402ad6a"
package_config:
  name: "biobox"
  version: "add_sgdemux"
  description: "A collection of bioinformatics tools for working with sequence data.\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 := 'add_sgdemux'"
  keywords:
  - "bioinformatics"
  - "modules"
  - "sequencing"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/biobox"
    issue_tracker: "https://github.com/viash-hub/biobox/issues"
