name: "star_genome_generate"
namespace: "star"
version: "v0.2.0"
authors:
- name: "Sai Nirmayi Yasa"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "nirmayi@data-intuitive.com"
      github: "sainirmayi"
      linkedin: "sai-nirmayi-yasa"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Junior Bioinformatics Researcher"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--genome_fasta_files"
    description: "Path(s) to the fasta files with the genome sequences, separated\
      \ by spaces. These files should be plain text FASTA files, they *cannot* be\
      \ zipped.\n"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--sjdb_gtf_file"
    description: "Path to the GTF file with annotations"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--sjdb_overhang"
    description: "Length of the donor/acceptor sequence on each side of the junctions,\
      \ ideally = (mate_length - 1)"
    info: null
    example:
    - 100
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sjdb_gtf_chr_prefix"
    description: "Prefix for chromosome names in a GTF file (e.g. 'chr' for using\
      \ ENSMEBL annotations with UCSC genomes)"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sjdb_gtf_feature_exon"
    description: "Feature type in GTF file to be used as exons for building transcripts"
    info: null
    example:
    - "exon"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sjdb_gtf_tag_exon_parent_transcript"
    description: "GTF attribute name for parent transcript ID (default \"transcript_id\"\
      \ works for GTF files)"
    info: null
    example:
    - "transcript_id"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sjdb_gtf_tag_exon_parent_gene"
    description: "GTF attribute name for parent gene ID (default \"gene_id\" works\
      \ for GTF files)"
    info: null
    example:
    - "gene_id"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sjdb_gtf_tag_exon_parent_gene_name"
    description: "GTF attribute name for parent gene name"
    info: null
    example:
    - "gene_name"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--sjdb_gtf_tag_exon_parent_gene_type"
    description: "GTF attribute name for parent gene type"
    info: null
    example:
    - "gene_type"
    - "gene_biotype"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "long"
    name: "--limit_genome_generate_ram"
    description: "Maximum available RAM (bytes) for genome generation"
    info: null
    example:
    - 31000000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--genome_sa_index_nbases"
    description: "Length (bases) of the SA pre-indexing string. Typically between\
      \ 10 and 15. Longer strings will use much more memory, but allow faster searches.\
      \ For small genomes, this parameter must be scaled down to min(14, log2(GenomeLength)/2\
      \ - 1)."
    info: null
    example:
    - 14
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--genome_chr_bin_nbits"
    description: "Defined as log2(chrBin), where chrBin is the size of the bins for\
      \ genome storage. Each chromosome will occupy an integer number of bins. For\
      \ a genome with large number of contigs, it is recommended to scale this parameter\
      \ as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)])."
    info: null
    example:
    - 18
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--genome_sa_sparse_d"
    description: "Suffux array sparsity, i.e. distance between indices. Use bigger\
      \ numbers to decrease needed RAM at the cost of mapping speed reduction."
    info: null
    example:
    - 1
    required: false
    min: 0
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--genome_suffix_length_max"
    description: "Maximum length of the suffixes, has to be longer than read length.\
      \ Use -1 for infinite length."
    info: null
    example:
    - -1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--genome_transform_type"
    description: "Type of genome transformation\n  None       ... no transformation\n\
      \  Haploid    ... replace reference alleles with alternative alleles from VCF\
      \ file (e.g. consensus allele)\n  Diploid    ... create two haplotypes for each\
      \ chromosome listed in VCF file, for genotypes 1|2, assumes perfect phasing\
      \ (e.g. personal genome)\n"
    info: null
    example:
    - "None"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_transform_vcf"
    description: "path to VCF file for genome transformation"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--index"
    description: "STAR index directory."
    info: null
    default:
    - "STAR_index"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Create index for STAR\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "genome"
- "index"
- "align"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/bts635"
links:
  repository: "https://github.com/alexdobin/STAR"
  documentation: "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf"
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: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "apt-get update && \\\n  apt-get install -y --no-install-recommends ${PACKAGES}\
      \ && \\\n  cd /tmp && \\\n  wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip\
      \ && \\\n  unzip ${STAR_VERSION}.zip && \\\n  cd STAR-${STAR_VERSION}/source\
      \ && \\\n  make STARstatic CXXFLAGS_SIMD=-std=c++11 && \\\n  cp STAR /usr/local/bin\
      \ && \\\n  cd / && \\\n  rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip\
      \ && \\\n  apt-get --purge autoremove -y ${PACKAGES} && \\\n  apt-get clean\n"
    env:
    - "STAR_VERSION 2.7.11b"
    - "PACKAGES gcc g++ make wget zlib1g-dev unzip xxd"
  - type: "docker"
    run:
    - "STAR --version | sed 's#\\(.*\\)#star: \"\\1\"#' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/star/star_genome_generate/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/star/star_genome_generate"
  executable: "target/executable/star/star_genome_generate/star_genome_generate"
  viash_version: "0.9.0"
  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
package_config:
  name: "biobox"
  version: "v0.2.0"
  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 := 'v0.2.0'"
  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"
