biobox/target/executable/fastqc/.config.vsh.yaml

name: "fastqc"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "theodorogtc@gmail.com"
      github: "tgaspe"
      linkedin: "theodoro-gasperin-terra-camargo"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "FASTQ file(s) to be analyzed.\n"
    info: null
    example:
    - "input.fq"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Outputs"
  description: "At least one of the output options (--html, --zip, --summary, --data)\
    \ must be used.\n"
  arguments:
  - type: "file"
    name: "--html"
    description: "Create the HTML report of the results. \n'*' wild card must be provided\
      \ in the output file name. \nWild card will be replaced by the input file basename.\n\
      e.g. \n  --input \"sample_1.fq\"\n  --html \"*.html\"\n  would create an output\
      \ html file named sample_1.html\n"
    info: null
    example:
    - "*.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--zip"
    description: "Create the zip file(s) containing: html report, data, images, icons,\
      \ summary, etc.\n'*' wild card must be provided in the output file name.\nWild\
      \ card will be replaced by the input basename.\ne.g. \n  --input \"sample_1.fq\"\
      \n  --html \"*.zip\"\n  would create an output zip file named sample_1.zip\n"
    info: null
    example:
    - "*.zip"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--summary"
    description: "Create the summary file(s).\n'*' wild card must be provided in the\
      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
      \ \n  --input \"sample_1.fq\"\n  --summary \"*_summary.txt\"\n  would create\
      \ an output summary.txt file named sample_1_summary.txt\n"
    info: null
    example:
    - "*_summary.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--data"
    description: "Create the data file(s).\n'*' wild card must be provided in the\
      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
      \ \n  --input \"sample_1.fq\"\n  --summary \"*_data.txt\"\n  would create an\
      \ output data.txt file named sample_1_data.txt\n"
    info: null
    example:
    - "*_data.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: true
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--casava"
    description: "Files come from raw casava output. Files in the same sample\ngroup\
      \ (differing only by the group number) will be analysed\nas a set rather than\
      \ individually. Sequences with the filter\nflag set in the header will be excluded\
      \ from the analysis.\nFiles must have the same names given to them by casava\n\
      (including being gzipped and ending with .gz) otherwise they\nwon't be grouped\
      \ together correctly.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--nano"
    description: "Files come from nanopore sequences and are in fast5 format. In\n\
      this mode you can pass in directories to process and the program\nwill take\
      \ in all fast5 files within those directories and produce\na single output file\
      \ from the sequences found in all files.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--nofilter"
    description: "If running with --casava then don't remove read flagged by\ncasava\
      \ as poor quality when performing the QC analysis.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--nogroup"
    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
      \ data for every base in the read. \nWARNING: Using this option will cause fastqc\
      \ to crash \nand burn if you use it on really long reads, and your \nplots may\
      \ end up a ridiculous size. You have been warned!\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--min_length"
    description: "Sets an artificial lower limit on the length of the \nsequence to\
      \ be shown in the report. As long as you \nset this to a value greater or equal\
      \ to your longest \nread length then this will be the sequence length used \n\
      to create your read groups. This can be useful for making\ndirectly comparable\
      \ statistics from datasets with somewhat \nvariable read lengths.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--format"
    alternatives:
    - "-f"
    description: "Bypasses the normal sequence file format detection and \nforces\
      \ the program to use the specified format. \nValid formats are bam, sam, bam_mapped,\
      \ sam_mapped, and fastq.\n"
    info: null
    example:
    - "bam"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--contaminants"
    alternatives:
    - "-c"
    description: "Specifies a non-default file which contains the list \nof contaminants\
      \ to screen overrepresented sequences against. \nThe file must contain sets\
      \ of named contaminants in the form\nname[tab]sequence. Lines prefixed with\
      \ a hash will be ignored.\n"
    info: null
    example:
    - "contaminants.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--adapters"
    alternatives:
    - "-a"
    description: "Specifies a non-default file which contains the list of \nadapter\
      \ sequences which will be explicitly searched against \nthe library. The file\
      \ must contain sets of named adapters \nin the form name[tab]sequence. Lines\
      \ prefixed with a hash will be ignored.\n"
    info: null
    example:
    - "adapters.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--limits"
    alternatives:
    - "-l"
    description: "Specifies a non-default file which contains \na set of criteria\
      \ which will be used to determine \nthe warn/error limits for the various modules.\
      \ \nThis file can also be used to selectively remove \nsome modules from the\
      \ output altogether. The format \nneeds to mirror the default limits.txt file\
      \ found in \nthe Configuration folder.\n"
    info: null
    example:
    - "limits.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--kmers"
    alternatives:
    - "-k"
    description: "Specifies the length of Kmer to look for in the Kmer \ncontent module.\
      \ Specified Kmer length must be between \n2 and 10. Default length is 7 if not\
      \ specified.\n"
    info: null
    example:
    - 7
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--quiet"
    alternatives:
    - "-q"
    description: "Suppress all progress messages on stdout and only report errors.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "FastQC - A high throughput sequence QC analysis tool."
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "Quality control"
- "BAM"
- "SAM"
- "FASTQ"
license: "GPL-3.0, Apache-2.0"
links:
  repository: "https://github.com/s-andrews/FastQC"
  homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
  documentation: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
  issue_tracker: "https://github.com/s-andrews/FastQC/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: "biocontainers/fastqc:v0.11.9_cv8"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "echo \"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/fastqc/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
  git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
  git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-3-g7f8bcc2"
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"