name: "samtools_fastq"
namespace: "samtools"
version: "main"
authors:
- name: "Emma Rousseau"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "emma@data-intuitive.com"
      github: "emmarousseau"
      linkedin: "emmarousseau1"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "input SAM/BAM/CRAM file"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "output FASTQ file"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--no_suffix"
    alternatives:
    - "-n"
    description: "By default, either '/1' or '/2' is added to the end of read names\
      \ where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes\
      \ read names to be left as they are.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--suffix"
    alternatives:
    - "-N"
    description: "Always add either '/1' or '/2' to the end of read names even when\
      \ put into different files.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--use_oq"
    alternatives:
    - "-O"
    description: "Use quality values from OQ tags in preference to standard quality\
      \ string if available.\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--singleton"
    alternatives:
    - "-s"
    description: "write singleton reads to FILE."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--copy_tags"
    alternatives:
    - "-t"
    description: "Copy RG, BC and QT tags to the FASTQ header line, if they exist.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--copy_tags_list"
    alternatives:
    - "-T"
    description: "Specify a comma-separated list of tags to copy to the FASTQ header\
      \ line, if they exist. \nTAGLIST can be blank or `*` to indicate all tags should\
      \ be copied to the output. If using `*`, \nbe careful to quote it to avoid unwanted\
      \ shell expansion.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read1"
    alternatives:
    - "-1"
    description: "Write reads with the READ1 FLAG set (and READ2 not set) to FILE\
      \ instead of outputting them. \nIf the -s option is used, only paired reads\
      \ will be written to this file.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read2"
    alternatives:
    - "-2"
    description: "Write reads with the READ2 FLAG set (and READ1 not set) to FILE\
      \ instead of outputting them. \nIf the -s option is used, only paired reads\
      \ will be written to this file.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_reads"
    alternatives:
    - "-o"
    description: "Write reads with either READ1 FLAG or READ2 flag set to FILE instead\
      \ of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_reads_both"
    alternatives:
    - "0"
    description: "Write reads where the READ1 and READ2 FLAG bits set are either both\
      \ set or both unset to FILE \ninstead of outputting them.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--filter_flags"
    alternatives:
    - "-f"
    description: "Only output alignments with all bits set in INT present in the FLAG\
      \ field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
      \ or in octal by beginning with '0'\n(i.e. /^0[0-7]+/). Default: `0`.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--excl_flags"
    alternatives:
    - "-F"
    description: "Do not output alignments with any bits set in INT present in the\
      \ FLAG field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
      \ or in octal by beginning with '0' \n(i.e. /^0[0-7]+/). This defaults to 0x900\
      \ representing filtering of secondary and \nsupplementary alignments. Default:\
      \ `0x900`.\n"
    info: null
    example:
    - "0x900"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--incl_flags"
    alternatives:
    - "--rf"
    description: "Only output alignments with any bits set in INT present in the FLAG\
      \ field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/),\
      \ in octal by beginning with '0'\n(i.e. /^0[0-7]+/), as a decimal number not\
      \ beginning with '0' or as a comma-separated list of \nflag names. Default:\
      \ `0`.\n"
    info: null
    example:
    - "0"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--excl_flags_all"
    alternatives:
    - "-G"
    description: "Only EXCLUDE reads with all of the bits set in INT present in the\
      \ FLAG field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
      \ or in octal by beginning with '0' (i.e. /^0[0-7]+/).\nDefault: `0`.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--aux_tag"
    alternatives:
    - "-d"
    description: "Only output alignments containing an auxiliary tag matching both\
      \ TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types\
      \ supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is\
      \ comparable to the method used in samtools view --tag. The option may be specified\
      \ \nmultiple times and is equivalent to using the --aux_tag_file option.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--aux_tag_file"
    alternatives:
    - "-D"
    description: "Only output alignments containing an auxiliary tag matching TAG\
      \ and having a value listed in FILE. \nThe format of the file is one line per\
      \ value. This is equivalent to specifying --aux_tag multiple times.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--casava"
    alternatives:
    - "-i"
    description: "Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--compression"
    alternatives:
    - "-c"
    description: "set compression level when writing gz or bgzf fastq files."
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--index1"
    alternatives:
    - "--i1"
    description: "write first index reads to FILE."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--index2"
    alternatives:
    - "--i2"
    description: "write second index reads to FILE."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--barcode_tag"
    description: "Auxiliary tag to find index reads in. Default: `BC`.\n"
    info: null
    example:
    - "BC"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--quality_tag"
    description: "Auxiliary tag to find index quality in. Default: `QT`.\n"
    info: null
    example:
    - "QT"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--index_format"
    description: "string to describe how to parse the barcode and quality tags. For\
      \ example:\n* `i14i8`: the first 14 characters are index 1, the next 8 characters\
      \ are index 2.\n* `n8i14`: ignore the first 8 characters, and use the next 14\
      \ characters for index 1.\nIf the tag contains a separator, then the numeric\
      \ part can be replaced with '*' to mean \n'read until the separator or end of\
      \ tag', for example: `n*i*`.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Converts a SAM, BAM or CRAM to FASTQ format."
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"
- "bam"
- "sam"
- "cram"
license: "MIT/Expat"
references:
  doi:
  - "10.1093/bioinformatics/btp352"
  - "10.1093/gigascience/giab008"
links:
  repository: "https://github.com/samtools/samtools"
  homepage: "https://www.htslib.org/"
  documentation: "https://www.htslib.org/doc/samtools-fastq.html"
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/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \\\nsed 's#Using\
      \ ##;s# \\([0-9\\.]*\\)$#: \\1#' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/samtools/samtools_fastq/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/samtools/samtools_fastq"
  executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
  viash_version: "0.9.0-RC6"
  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
  git_remote: "https://github.com/viash-hub/biobox"
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-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 := '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"