name: "falco"
version: "seqtk_sample"
argument_groups:
- name: "Input arguments"
  arguments:
  - type: "file"
    name: "--input"
    description: "input fastq files"
    info: null
    example:
    - "input1.fastq;input2.fastq"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Run arguments"
  arguments:
  - type: "boolean_true"
    name: "--nogroup"
    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
      \ data for every base in \nthe read. WARNING: When using this option, \nyour\
      \ plots may end up a ridiculous size. You \nhave been warned!\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--contaminents"
    description: "Specifies a non-default file which contains \nthe list of contaminants\
      \ to screen \noverrepresented sequences against. The file \nmust contain sets\
      \ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\
      \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--adapters"
    description: "Specifies a non-default file which contains \nthe list of adapter\
      \ sequences which will be \nexplicity searched against the library. The \nfile\
      \ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\
      \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--limits"
    description: "Specifies a non-default file which contains \na set of criteria\
      \ which will be used to \ndetermine the warn/error limits for the \nvarious\
      \ modules. This file can also be used \nto selectively remove some modules from\
      \ the \noutput all together. The format needs to \nmirror the default limits.txt\
      \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--subsample"
    alternatives:
    - "-s"
    description: "[Falco only] makes falco faster (but \npossibly less accurate) by\
      \ only processing \nreads that are a multiple of this value (using \n0-based\
      \ indexing to number reads).\n"
    info: null
    example:
    - 10
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--bisulfite"
    alternatives:
    - "-b"
    description: "[Falco only] reads are whole genome \nbisulfite sequencing, and\
      \ more Ts and fewer \nCs are therefore expected and will be \naccounted for\
      \ in base content.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--reverse_complliment"
    alternatives:
    - "-r"
    description: "[Falco only] The input is a \nreverse-complement. All modules will\
      \ be \ntested by swapping A/T and C/G\n"
    info: null
    direction: "input"
- name: "Output arguments"
  arguments:
  - type: "file"
    name: "--outdir"
    alternatives:
    - "-o"
    description: "Create all output files in the specified \noutput directory. FALCO-SPECIFIC:\
      \ If the \ndirectory does not exists, the program will \ncreate it.\n"
    info: null
    example:
    - "output"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--format"
    alternatives:
    - "-f"
    description: "Bypasses the normal sequence file format \ndetection and forces\
      \ the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped,\
      \ sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n"
    info: null
    required: false
    choices:
    - "bam"
    - "sam"
    - "bam_mapped"
    - "sam_mapped"
    - "fastq"
    - "fq"
    - "fastq.gz"
    - "fq.gz"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--data_filename"
    alternatives:
    - "-D"
    description: "[Falco only] Specify filename for FastQC \ndata output (TXT). If\
      \ not specified, it will \nbe called fastq_data.txt in either the input \nfile's\
      \ directory or the one specified in the \n--output flag. Only available when\
      \ running \nfalco with a single input.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--report_filename"
    alternatives:
    - "-R"
    description: "[Falco only] Specify filename for FastQC \nreport output (HTML).\
      \ If not specified, it \nwill be called fastq_report.html in either \nthe input\
      \ file's directory or the one \nspecified in the --output flag. Only \navailable\
      \ when running falco with a single \ninput.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--summary_filename"
    alternatives:
    - "-S"
    description: "[Falco only] Specify filename for the short \nsummary output (TXT).\
      \ If not specified, it \nwill be called fastq_report.html in either \nthe input\
      \ file's directory or the one \nspecified in the --output flag. Only \navailable\
      \ when running falco with a single \ninput.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "A C++ drop-in replacement of FastQC to assess the quality of sequence\
  \ read data"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "qc"
- "fastqc"
- "sequencing"
license: "GPL-3.0"
references:
  doi:
  - "10.12688/f1000research.21142.2"
links:
  repository: "https://github.com/smithlabcode/falco"
  documentation: "https://falco.readthedocs.io/en/latest/"
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: "debian:trixie-slim"
  target_registry: "images.viash-hub.com"
  target_tag: "seqtk_sample"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "wget"
    - "build-essential"
    - "g++"
    - "zlib1g-dev"
    - "procps"
    interactive: false
  - type: "docker"
    run:
    - "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz\
      \ -O /tmp/falco.tar.gz && \\\ncd /tmp && \\\ntar xvf falco.tar.gz && \\\ncd\
      \ falco-1.2.2 && \\\n./configure && \\\nmake all && \\\nmake install\n"
  - type: "docker"
    run:
    - "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/falco/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/falco"
  executable: "target/nextflow/falco/main.nf"
  viash_version: "0.9.0-RC6"
  git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
  git_remote: "https://github.com/viash-hub/biobox"
package_config:
  name: "biobox"
  version: "seqtk_sample"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0-RC6"
  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 := 'seqtk_sample'"
  keywords:
  - "bioinformatics"
  - "sequence"
  - "alignment"
  - "variant calling"
  - "dna"
  - "rna"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/biobbox"
    issue_tracker: "https://github.com/viash-hub/biobox/issues"
