name: "kallisto_quant"
namespace: "kallisto"
version: "main"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--input"
    description: "List of input FastQ files of size 1 and 2 for single-end and paired-end\
      \ data, respectively."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--index"
    alternatives:
    - "-i"
    description: "Kallisto genome index."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--output_dir"
    alternatives:
    - "-o"
    description: "Directory to write output to."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--log"
    description: "File containing log information from running kallisto quant"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--single"
    description: "Single end mode."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--single_overhang"
    description: "Include reads where unobserved rest of fragment is predicted to\
      \ lie outside a transcript."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--fr_stranded"
    description: "Strand specific reads, first read forward."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--rf_stranded"
    description: "Strand specific reads, first read reverse."
    info: null
    direction: "input"
  - type: "double"
    name: "--fragment_length"
    alternatives:
    - "-l"
    description: "The estimated average fragment length."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--sd"
    alternatives:
    - "-s"
    description: "The estimated standard deviation of the fragment length (default:\
      \ -l, -s values are estimated \nfrom paired end data, but are required when\
      \ using --single).\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--plaintext"
    description: "Output plaintext instead of HDF5."
    info: null
    direction: "input"
  - type: "integer"
    name: "--bootstrap_samples"
    alternatives:
    - "-b"
    description: "Number of bootstrap samples to draw. Default: '0'\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--seed"
    description: "Random seed for bootstrap. Default: '42'\n"
    info: null
    example:
    - 42
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally\
  \ of target sequences using high-throughput sequencing reads.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "kallisto"
- "quant"
- "pseudoalignment"
license: "BSD 2-Clause License"
references:
  doi:
  - "10.1038/nbt.3519"
links:
  repository: "https://github.com/pachterlab/kallisto"
  homepage: "https://pachterlab.github.io/kallisto/about"
  documentation: "https://pachterlab.github.io/kallisto/manual"
  issue_tracker: "https://github.com/pachterlab/kallisto/issues"
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: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "apt-get update && \\\napt-get install -y --no-install-recommends wget && \\\
      \nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
      \ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
      \ /usr/local/bin/\n"
  - type: "docker"
    run:
    - "echo \"kallisto: $(kallisto version | sed 's/kallisto, version //')\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/kallisto/kallisto_quant/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/kallisto/kallisto_quant"
  executable: "target/nextflow/kallisto/kallisto_quant/main.nf"
  viash_version: "0.9.0"
  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g952ff08"
package_config:
  name: "biobox"
  version: "main"
  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 := 'main'"
  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"
