name: "snpeff"
version: "add_sgdemux"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "Input variants file."
    info: null
    example:
    - "test.vcf"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--genome_version"
    description: "Reference genome version."
    info: null
    example:
    - "GRCh37.75"
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "The output file."
    info: null
    example:
    - "out.vcf"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--summary"
    description: "Summary file directory."
    info: null
    example:
    - "summary_dir"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genes"
    description: "Txt file directory."
    info: null
    example:
    - "genes_dir"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "string"
    name: "--chr"
    description: "Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1').\
      \ Only on TXT output.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--classic"
    description: "Use old style annotations instead of Sequence Ontology and Hgvs."
    info: null
    direction: "input"
  - type: "file"
    name: "--csv_stats"
    description: "Create CSV summary file."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--download"
    description: "Download reference genome if not available."
    info: null
    direction: "input"
  - type: "string"
    name: "--input_format"
    alternatives:
    - "-i"
    description: "Input format [ vcf, bed ]. Default: VCF.\nexample: \"VCF\"\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--file_list"
    description: "Input actually contains a list of files to process."
    info: null
    direction: "input"
  - type: "string"
    name: "--output_format"
    alternatives:
    - "-o"
    description: "Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n"
    info: null
    example:
    - "VCF"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--stats"
    alternatives:
    - "-s"
    - "--htmlStats"
    description: "Create HTML summary file."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_stats"
    description: "Do not create stats (summary) file."
    info: null
    direction: "input"
- name: "Results filter options"
  arguments:
  - type: "file"
    name: "--fi"
    alternatives:
    - "--filterInterval"
    description: "Only analyze changes that intersect with the intervals \nspecified\
      \ in this file. This option can be used several times.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_downstream"
    description: "Do not show DOWNSTREAM changes"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_intergenic"
    description: "Do not show INTERGENIC changes."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_intron"
    description: "Do not show INTRON changes."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_upstream"
    description: "Do not show UPSTREAM changes."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_utr"
    description: "Do not show 5_PRIME_UTR or 3_PRIME_UTR changes."
    info: null
    direction: "input"
  - type: "string"
    name: "--no"
    description: "Do not show 'EffectType'. This option can be used several times.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Annotations options"
  arguments:
  - type: "boolean_true"
    name: "--cancer"
    description: "Perform 'cancer' comparisons (Somatic vs Germline)."
    info: null
    direction: "input"
  - type: "file"
    name: "--cancer_samples"
    description: "Two column TXT file defining 'original \\t derived' samples."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastaprot"
    description: "Create an output file containing the resulting protein sequences.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--format_eff"
    description: "Use 'EFF' field compatible with older versions (instead of 'ANN').\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--gene_id"
    description: "Use gene ID instead of gene name (VCF output)."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--hgvs"
    description: "Use HGVS annotations for amino acid sub-field."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--hgvs_old"
    description: "Use old HGVS notation."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--hgvs1_letter_aa"
    description: "Use one letter Amino acid codes in HGVS notation."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--hgvs_tr_id"
    description: "Use transcript ID in HGVS notation."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--lof"
    description: "Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "-no_hgvs"
    description: "Do not add HGVS annotations."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_lof"
    description: "Do not add LOF and NMD annotations."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_shift_hgvs"
    description: "Do not shift variants according to HGVS notation (most 3prime end).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--oicr"
    description: "Add OICR tag in VCF file."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--sequence_ontology"
    description: "Use Sequence Ontology terms."
    info: null
    direction: "input"
- name: "Generic options"
  arguments:
  - type: "file"
    name: "--config"
    alternatives:
    - "-c"
    description: "Specify config file"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--config_option"
    description: "Override a config file option (name=value)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--debug"
    alternatives:
    - "-d"
    description: "Debug mode (very verbose)."
    info: null
    direction: "input"
  - type: "file"
    name: "--data_dir"
    description: "Override data_dir parameter from config file."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_download"
    description: "Do not download a SnpEff database, if not available locally."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_log"
    description: "Do not report usage statistics to server."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--quiet"
    alternatives:
    - "-q"
    description: "Quiet mode (do not show any messages or errors)"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--verbose"
    alternatives:
    - "-v"
    description: "Verbose mode."
    info: null
    direction: "input"
- name: "Database options"
  arguments:
  - type: "boolean_true"
    name: "--canon"
    description: "Only use canonical transcripts."
    info: null
    direction: "input"
  - type: "file"
    name: "--canon_list"
    description: "Only use canonical transcripts, replace some transcripts using the\
      \ 'gene_id         \ntranscript_id' entries in <file>.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--tag"
    description: "Only use transcript having a tag 'tagName'. This option can be used\
      \ multiple times.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_tag"
    description: "Filter out transcript having a tag 'tagName'. This option can be\
      \ used multiple times.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--interaction"
    description: "Annotate using interactions (requires interaction database)."
    info: null
    direction: "input"
  - type: "file"
    name: "--interval"
    description: "Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use\
      \ this option many times).\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_tsl"
    description: "Only use transcripts having Transcript Support Level lower than\
      \ <TSL_number>."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--motif"
    description: "Annotate using motifs (requires Motif database)."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--nextprot"
    description: "Annotate using NextProt (requires NextProt database)."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_genome"
    description: "Do not load any genomic database (e.g. annotate using custom files)."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_expand_iub"
    description: "Disable IUB code expansion in input variants."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_interaction"
    description: "Disable inteaction annotations."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_motif"
    description: "Disable motif annotations."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_nextprot"
    description: "Disable NextProt annotations."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--only_reg"
    description: "Only use regulation tracks."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--only_protein"
    description: "Only use protein coding transcripts."
    info: null
    direction: "input"
  - type: "file"
    name: "--only_tr"
    description: "Only use the transcripts in this file. Format: One transcript ID\
      \ per line.\n"
    info: null
    example:
    - "file.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--reg"
    description: "Regulation track to use (this option can be used add several times)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--ss"
    alternatives:
    - "--spliceSiteSize"
    description: "Set size for splice sites (donor and acceptor) in bases. Default:\
      \ 2.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--splice_region_exon_size"
    description: "Set size for splice site region within exons. Default: 3 bases.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--splice_region_intron_min"
    description: "Set minimum number of bases for splice site region within intron.\
      \ Default: 3 bases.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--splice_region_intron_max"
    description: "Set maximum number of bases for splice site region within intron.\
      \ Default: 8 bases.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--strict"
    description: "Only use 'validated' transcripts (i.e. sequence has been checked)."
    info: null
    direction: "input"
  - type: "integer"
    name: "--ud"
    alternatives:
    - "--upDownStreamLen"
    description: "Set upstream downstream interval length (in bases)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Genetic variant annotation, and functional effect prediction toolbox.\
  \ \nIt annotates and predicts the effects of genetic variants on genes and \nproteins\
  \ (such as amino acid changes).\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:
- "annotation"
- "effect prediction"
- "snp"
- "variant"
- "vcf"
license: "MIT"
references:
  doi:
  - "10.3389/fgene.2012.00035"
links:
  repository: "https://github.com/pcingola/SnpEff"
  homepage: "https://pcingola.github.io/SnpEff/"
  documentation: "https://pcingola.github.io/SnpEff/"
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/staphb/snpeff:5.2a"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "version=$(snpEff -version) && \\\nversion_trimmed=$(echo \"$version\" | awk\
      \ '{print $1, $2}') && \\\necho \"$version_trimmed\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/snpeff/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/snpeff"
  executable: "target/executable/snpeff/snpeff"
  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"
