biobox/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml

name: "bedtools_getfasta"
namespace: "bedtools"
version: "main"
authors:
- name: "Dries Schaumont"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "dries@data-intuitive.com"
      github: "DriesSchaumont"
      orcid: "0000-0002-4389-0440"
      linkedin: "dries-schaumont"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
argument_groups:
- name: "Input arguments"
  arguments:
  - type: "file"
    name: "--input_fasta"
    description: "FASTA file containing sequences for each interval specified in the\
      \ input BED file.\nThe headers in the input FASTA file must exactly match the\
      \ chromosome column in the BED file.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_bed"
    description: "BED file containing intervals to extract from the FASTA file.\n\
      BED files containing a single region require a newline character\nat the end\
      \ of the line, otherwise a blank output file is produced.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--rna"
    description: "The FASTA is RNA not DNA. Reverse complementation handled accordingly.\n"
    info: null
    direction: "input"
- name: "Run arguments"
  arguments:
  - type: "boolean_true"
    name: "--strandedness"
    alternatives:
    - "-s"
    description: "Force strandedness. If the feature occupies the antisense strand,\
      \ the output sequence will\nbe reverse complemented. By default strandedness\
      \ is not taken into account.\n"
    info: null
    direction: "input"
- name: "Output arguments"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-o"
    description: "Output file where the output from the 'bedtools getfasta' commend\
      \ will\nbe written to.\n"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--tab"
    description: "Report extract sequences in a tab-delimited format instead of in\
      \ FASTA format.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed_out"
    description: "Report extract sequences in a tab-delimited BED format instead of\
      \ in FASTA format.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--name"
    description: "Set the FASTA header for each extracted sequence to be the \"name\"\
      \ and coordinate columns from the BED feature.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--name_only"
    description: "Set the FASTA header for each extracted sequence to be the \"name\"\
      \ columns from the BED feature.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--split"
    description: "When --input is in BED12 format, create a separate fasta entry for\
      \ each block in a BED12 record,\nblocks being described in the 11th and 12th\
      \ column of the BED.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--full_header"
    description: "Use full fasta header. By default, only the word before the first\
      \ space or tab is used.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Extract sequences from a FASTA file for each of the intervals defined\
  \ in a BED/GFF/VCF file."
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "sequencing"
- "fasta"
- "BED"
- "GFF"
- "VCF"
license: "GPL-2.0"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.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: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "bedtools"
    - "procps"
    interactive: false
  - type: "docker"
    run:
    - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
      \ > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_getfasta/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  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"