name: "nanoplot"
version: "add_sgdemux"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--fastq"
    description: "Input fastq file(s), separated by \";\"."
    info: null
    example:
    - "read.fq"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--fasta"
    description: "Input fasta file(s), separated by \";\"."
    info: null
    example:
    - "read.fa"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--fastq_rich"
    description: "Input fastq file(s) generated by albacore or \nMinKNOW with additional\
      \ information concerning channel and time, separated by \";\".\n"
    info: null
    example:
    - "read.fq"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--fastq_minimal"
    description: "Input fastq file(s) generated by albacore or MinKNOW with\nadditional\
      \ information concerning channel and time. Minimal data is extracted\nswiftly\
      \ without elaborate checks. Separated by \";\".\n"
    info: null
    example:
    - "read.fq"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--summary"
    description: "Input summary file(s) generated by albacore or guppy, separated\
      \ by \";\".\n"
    info: null
    example:
    - "read.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--bam"
    description: "Input sorted bam file(s), separated by \";\"."
    info: null
    example:
    - "read.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--ubam"
    description: "Input unmapped bam file(s), separated by \";\"."
    info: null
    example:
    - "read.ubam"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--cram"
    description: "Input sorted cram file(s), separated by \";\"."
    info: null
    example:
    - "read.cram"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--pickle"
    description: "Input pickle file stored earlier, separated by \";\"."
    info: null
    example:
    - "read.pkl"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--feather"
    alternatives:
    - "--arrow"
    description: "Input feather file(s), separated by \";\"."
    info: null
    example:
    - "read.arrow"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--outdir"
    alternatives:
    - "-o"
    description: "Specify directory in which output has to be created."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--verbose"
    description: "Write log messages also to terminal"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--store"
    description: "Store the extracted data in a pickle file for future plotting."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--raw"
    description: "Store the extracted data in tab separated file."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--huge"
    description: "Input data is one very large file."
    info: null
    direction: "input"
  - type: "boolean_false"
    name: "--no_static"
    description: "Do not make static (png) plots."
    info: null
    direction: "input"
  - type: "string"
    name: "--prefix"
    alternatives:
    - "-p"
    description: "Specify an optional prefix to be used for the output files."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--tsv_stats"
    description: "Output the stats file as a properly formatted TSV."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--only_report"
    description: "Output only the report."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--info_in_report"
    description: "Add NanoPlot run info in the report."
    info: null
    direction: "input"
- name: "Filtering or transforming input"
  arguments:
  - type: "integer"
    name: "--maxlength"
    description: "Drop reads longer than length specified."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--minlength"
    description: "Drop reads shorter than length specified."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_false"
    name: "--drop_outliers"
    description: "Drop outlier reads with extreme long length."
    info: null
    direction: "input"
  - type: "integer"
    name: "--downsample"
    description: "Reduce dataset to N reads by random sampling."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--loglength"
    description: "Logarithmic scaling of lengths in plots."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--percentqual"
    description: "Use qualities as theoretical percent identities."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--alength"
    description: "Use aligned read lengths rather than sequenced length (bam mode)."
    info: null
    direction: "input"
  - type: "integer"
    name: "--minqual"
    description: "Drop reads with an average quality lower than specified."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--runtime_until"
    description: "Only take the N first hours of a run."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--readtype"
    description: "Which read type to extract information about from summary.\nOptions\
      \ are 1D, 2D, 1D2\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--barcoded"
    description: "Use if you want to split the summary file by barcode."
    info: null
    direction: "input"
  - type: "boolean_false"
    name: "--no_supplementary"
    description: "Use if you want to remove supplementary alignments."
    info: null
    direction: "input"
- name: "Customizing plots"
  arguments:
  - type: "string"
    name: "--color"
    alternatives:
    - "-c"
    description: "Specify a color for the plots, must be a valid matplotlib color."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--colormap"
    alternatives:
    - "-cm"
    description: "Specify a valid matplotlib colormap for the heatmap."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--format"
    alternatives:
    - "-f"
    description: "Specify the output format of the plots.\n{eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}\n"
    info: null
    default:
    - "png"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--plots"
    description: "Specify which bivariate plots have to be made.\n[{kde,hex,dot} ...]\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--legacy"
    description: "Specify which bivariate plots have to be made (legacy mode).\n[{kde,dot,hex}\
      \ ...]\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--listcolors"
    description: "List the colors which are available for plotting and exit."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--listcolormaps"
    description: "List the colormaps which are available for plotting and exit."
    info: null
    direction: "input"
  - type: "boolean_false"
    name: "--no_N50"
    description: "Hide the N50 mark in the read length histogram."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--N50"
    description: "Show the N50 mark in the read length histogram."
    info: null
    direction: "input"
  - type: "string"
    name: "--title"
    description: "Add a title to all plots, requires quoting if using spaces."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--font_scale"
    description: "Scale the font of the plots by a factor."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--dpi"
    description: "Set the dpi for saving images."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_false"
    name: "--hide_stats"
    description: "Not adding Pearson R stats in some bivariate plots."
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Run NanoPlot on nanopore-sequenced reads.\nNanoPlot is a plotting tool\
  \ for long read sequencing data and alignments.\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:
- "fastq"
- "sequencing summary"
- "nanopore"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btad311"
links:
  repository: "https://github.com/wdecoster/NanoPlot"
  homepage: "http://nanoplot.bioinf.be/"
  documentation: "https://github.com/wdecoster/NanoPlot"
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/nanoplot:1.43.0--pyhdfd78af_1"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "version=$(NanoPlot --version) && \\\necho \"$version\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/nanoplot/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/nanoplot"
  executable: "target/nextflow/nanoplot/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"
