name: "lofreq_call"
namespace: "lofreq"
version: "add_sgdemux"
authors:
- name: "Kai Waldrant"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "kai@data-intuitive.com"
      github: "KaiWaldrant"
      orcid: "0009-0003-8555-1361"
      linkedin: "kaiwaldrant"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
    - name: "Open Problems"
      href: "https://openproblems.bio"
      role: "Contributor"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "Input BAM file.\n"
    info: null
    example:
    - "normal.bam"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_bai"
    description: "Index file for the input BAM file.\n"
    info: null
    example:
    - "normal.bai"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--ref"
    alternatives:
    - "-f"
    description: "Indexed reference fasta file (gzip supported). Default: none.\n"
    info: null
    example:
    - "reference.fasta"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--out"
    alternatives:
    - "-o"
    description: "Vcf output file. Default: stdout.\n"
    info: null
    example:
    - "output.vcf"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Arguments"
  arguments:
  - type: "string"
    name: "--region"
    alternatives:
    - "-r"
    description: "Limit calls to this region (chrom:start-end). Default: none.\n"
    info: null
    example:
    - "chr1:1000-2000"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bed"
    alternatives:
    - "-l"
    description: "List of positions (chr pos) or regions (BED). Default: none.\n"
    info: null
    example:
    - "regions.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_bq"
    alternatives:
    - "-q"
    description: "Skip any base with baseQ smaller than INT. Default: 6.\n"
    info: null
    example:
    - 6
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_alt_bq"
    alternatives:
    - "-Q"
    description: "Skip alternate bases with baseQ smaller than INT. Default: 6.\n"
    info: null
    example:
    - 6
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--def_alt_bq"
    alternatives:
    - "-R"
    description: "Overwrite baseQs of alternate bases (that passed bq filter) with\
      \ this value (-1: use median ref-bq; 0: keep). Default: 0.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_jq"
    alternatives:
    - "-j"
    description: "Skip any base with joinedQ smaller than INT. Default: 0.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_alt_jq"
    alternatives:
    - "-J"
    description: "Skip alternate bases with joinedQ smaller than INT. Default: 0.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--def_alt_jq"
    alternatives:
    - "-K"
    description: "Overwrite joinedQs of alternate bases (that passed jq filter) with\
      \ this value (-1: use median ref-bq; 0: keep). Default: 0.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_baq"
    alternatives:
    - "-B"
    description: "Disable use of base-alignment quality (BAQ).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_idaq"
    alternatives:
    - "-A"
    description: "Don't use IDAQ values (NOT recommended under ANY circumstances other\
      \ than debugging).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--del_baq"
    alternatives:
    - "-D"
    description: "Delete pre-existing BAQ values, i.e. compute even if already present\
      \ in BAM.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_ext_baq"
    alternatives:
    - "-e"
    description: "Use 'normal' BAQ (samtools default) instead of extended BAQ (both\
      \ computed on the fly if not already present in lb tag).\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--min_mq"
    alternatives:
    - "-m"
    description: "Skip reads with mapping quality smaller than INT. Default: 0.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_mq"
    alternatives:
    - "-M"
    description: "Cap mapping quality at INT. Default: 255.\n"
    info: null
    example:
    - 255
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_mq"
    alternatives:
    - "-N"
    description: "Don't merge mapping quality in LoFreq's model.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--call_indels"
    description: "Enable indel calls (note: preprocess your file to include indel\
      \ alignment qualities!).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--only_indels"
    description: "Only call indels; no SNVs.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--src_qual"
    alternatives:
    - "-s"
    description: "Enable computation of source quality.\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--ign_vcf"
    alternatives:
    - "-S"
    description: "Ignore variants in this vcf file for source quality computation.\
      \ Multiple files can be given separated by commas.\n"
    info: null
    example:
    - "variants.vcf"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--def_nm_q"
    alternatives:
    - "-T"
    description: "If >= 0, then replace non-match base qualities with this default\
      \ value. Default: -1.\n"
    info: null
    example:
    - -1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--sig"
    alternatives:
    - "-a"
    description: "P-Value cutoff / significance level. Default: 0.010000.\n"
    info: null
    example:
    - 0.01
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--bonf"
    alternatives:
    - "-b"
    description: "Bonferroni factor. 'dynamic' (increase per actually performed test)\
      \ or INT. Default: Dynamic.\n"
    info: null
    example:
    - "dynamic"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_cov"
    alternatives:
    - "-C"
    description: "Test only positions having at least this coverage. Default: 1.\n\
      (note: without --no-default-filter default filters (incl. coverage) kick in\
      \ after predictions are done).\n"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_depth"
    alternatives:
    - "-d"
    description: "Cap coverage at this depth. Default: 1000000.\n"
    info: null
    example:
    - 1000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--illumina_13"
    description: "Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--use_orphan"
    description: "Count anomalous read pairs (i.e. where mate is not aligned properly).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--plp_summary_only"
    description: "No variant calling. Just output pileup summary per column.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_default_filter"
    description: "Don't run default 'lofreq filter' automatically after calling variants.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--force_overwrite"
    description: "Overwrite any existing output.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--verbose"
    description: "Be verbose.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--debug"
    description: "Enable debugging.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is\
  \ a fast and sensitive variant-caller for inferring SNVs and indels from next-generation\
  \ sequencing data. It makes full use of base-call qualities and other sources of\
  \ errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty),\
  \ which are usually ignored by other methods or only used for filtering.\n\nLoFreq*\
  \ can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent\
  \ or Pacbio) since no machine- or sequencing-technology dependent thresholds are\
  \ used. It automatically adapts to changes in coverage and sequencing quality and\
  \ can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial,\
  \ metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is\
  \ able to predict variants below the average base-call quality (i.e. sequencing\
  \ error rate). Each variant call is assigned a p-value which allows for rigorous\
  \ false positive control. Even though it uses no approximations or heuristics, it\
  \ is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel\
  \ implementation. LoFreq* is generic and fast enough to be applied to high-coverage\
  \ data and large genomes. On a single processor it takes a minute to analyze Dengue\
  \ genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs\
  \ on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage\
  \ human exome dataset.\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:
- "variant calling"
- "low frequancy variant calling"
- "lofreq"
- "lofreq/call"
license: "MIT"
references:
  doi:
  - "10.1093/nar/gks918"
links:
  repository: "https://github.com/viash-hub/biobox"
  homepage: "https://csb5.github.io/lofreq/"
  documentation: "https://csb5.github.io/lofreq/commands/"
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/lofreq:2.1.5--py38h794fc9e_10"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "version=$(lofreq version | grep 'version' | sed 's/version: //') && \\\necho\
      \ \"lofreq: $version\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/lofreq/call/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  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"
