name: "multiqc"
version: "add_sgdemux"
authors:
- name: "Dorien Roosen"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "dorien@data-intuitive.com"
      github: "dorien-er"
      linkedin: "dorien-roosen"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--input"
    description: "File paths to be searched for analysis results to be included in\
      \ the report.\n"
    info: null
    example:
    - "data/results"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Ouput"
  arguments:
  - type: "file"
    name: "--output_report"
    description: "Filepath of the generated report.\n"
    info: null
    example:
    - "multiqc_report.html"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_data"
    description: "Output directory for parsed data files. If not provided, parsed\
      \ data will not be published.\n"
    info: null
    example:
    - "multiqc_data"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_plots"
    description: "Output directory for generated plots. If not provided, plots will\
      \ not be published.\n"
    info: null
    example:
    - "multiqc_plots"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Modules and analyses to run"
  arguments:
  - type: "string"
    name: "--include_modules"
    description: "Use only these module"
    info: null
    example:
    - "fastqc"
    - "cutadapt"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--exclude_modules"
    description: "Do not use only these modules"
    info: null
    example:
    - "fastqc"
    - "cutadapt"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--ignore_analysis"
    info: null
    example:
    - "run_one/*"
    - "run_two/*"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--ignore_samples"
    info: null
    example:
    - "sample_1*"
    - "sample_3*"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--ignore_symlinks"
    description: "Ignore symlinked directories and files"
    info: null
    direction: "input"
- name: "Sample name handling"
  arguments:
  - type: "boolean_true"
    name: "--dirs"
    description: "Prepend directory to sample names to avoid clashing filenames"
    info: null
    direction: "input"
  - type: "integer"
    name: "--dirs_depth"
    description: "Prepend n directories to sample names. Negative number to take from\
      \ start of path."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--full_names"
    description: "Do not clean the sample names (leave as full file name)"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--fn_as_s_name"
    description: "Use the log filename as the sample name"
    info: null
    direction: "input"
  - type: "file"
    name: "--replace_names"
    description: "TSV file to rename sample names during report generation"
    info: null
    example:
    - "replace_names.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Report Customisation"
  arguments:
  - type: "string"
    name: "--title"
    description: "Report title. Printed as page header, used for filename if not otherwise\
      \ specified.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--comment"
    description: "Custom comment, will be printed at the top of the report.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--template"
    description: "Report template to use.\n"
    info: null
    required: false
    choices:
    - "default"
    - "gathered"
    - "geo"
    - "highcharts"
    - "sections"
    - "simple"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--sample_names"
    description: "TSV file containing alternative sample names for renaming buttons\
      \ in the report.\n"
    info: null
    example:
    - "sample_names.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--sample_filters"
    description: "TSV file containing show/hide patterns for the report\n"
    info: null
    example:
    - "sample_filters.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--custom_css_file"
    description: "Custom CSS file to add to the final report\n"
    info: null
    example:
    - "custom_style_sheet.css"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--profile_runtime"
    description: "Add analysis of how long MultiQC takes to run to the report\n"
    info: null
    direction: "input"
- name: "MultiQC behaviour"
  arguments:
  - type: "boolean_true"
    name: "--verbose"
    description: "Increase output verbosity.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--quiet"
    description: "Only show log warnings\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--strict"
    description: "Don't catch exceptions, run additional code checks to help development.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--development"
    description: "Development mode. Do not compress and minimise JS, export uncompressed\
      \ plot data.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--require_logs"
    description: "Require all explicitly requested modules to have log files. If not,\
      \ MultiQC will exit with an error.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_megaqc_upload"
    description: "Don't upload generated report to MegaQC, even if MegaQC options\
      \ are found.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_ansi"
    description: "Disable coloured log output.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--cl_config"
    description: "YAML formatted string that allows to customize MultiQC behaviour\
      \ like input file detection.\n"
    info: null
    example:
    - "qualimap_config: { general_stats_coverage: [20,40,200] }"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output format"
  arguments:
  - type: "boolean_true"
    name: "--flat"
    description: "Use only flat plots (static images).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--interactive"
    description: "Use only interactive plots (in-browser Javascript).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--data_dir"
    description: "Force the parsed data directory to be created.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_data_dir"
    description: "Prevent the parsed data directory from being created.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--zip_data_dir"
    description: "Compress the data directory.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--data_format"
    description: "Output parsed data in a different format than the default 'txt'.\n"
    info: null
    required: false
    choices:
    - "tsv"
    - "csv"
    - "json"
    - "yaml"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--pdf"
    description: "Creates PDF report with the 'simple' template. Requires Pandoc to\
      \ be installed.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "MultiQC aggregates results from bioinformatics analyses across many\
  \ samples into a single report.\nIt searches a given directory for analysis logs\
  \ and compiles a HTML report. It's a general use tool, perfect for summarising the\
  \ output from numerous bioinformatics tools.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info:
  keywords:
  - "QC"
  - "html report"
  - "aggregate analysis"
  links:
    homepage: "https://multiqc.info/"
    documentation: "https://multiqc.info/docs/"
    repository: "https://github.com/MultiQC/MultiQC"
  references:
    doi: "10.1093/bioinformatics/btw354"
  licence: "GPL v3 or later"
status: "enabled"
requirements:
  commands:
  - "ps"
license: "MIT"
links:
  repository: "https://github.com/viash-hub/biobox"
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/multiqc:1.21--pyhdfd78af_0"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "multiqc --version | sed 's/multiqc, version\\s\\(.*\\)/multiqc: \"\\1\"/' >\
      \ /var/software_versions.txt\n"
  test_setup:
  - type: "apt"
    packages:
    - "jq"
    interactive: false
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/multiqc/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/multiqc"
  executable: "target/nextflow/multiqc/main.nf"
  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"
