name: "salmon_index"
namespace: "salmon"
version: "main"
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: "Inputs"
  arguments:
  - type: "file"
    name: "--genome"
    description: "Genome of the organism to prepare the set of decoy sequences. Required\
      \ to build decoy-aware transcriptome.\n"
    info: null
    example:
    - "genome.fasta"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcripts"
    alternatives:
    - "-t"
    description: "Transcript fasta file.\n"
    info: null
    example:
    - "transcriptome.fasta"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--kmer_len"
    alternatives:
    - "-k"
    description: "The size of k-mers that should be used for the quasi index.\n"
    info: null
    example:
    - 31
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--gencode"
    description: "This flag will expect the input transcript fasta to be in GENCODE\
      \ format, and will split the transcript name at the first '|' character. These\
      \ reduced names will be used in the output and when looking for these transcripts\
      \ in a gene to transcript GTF.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--features"
    description: "This flag will expect the input reference to be in the tsv file\
      \ format, and will split the feature name at the first 'tab' character. These\
      \ reduced names will be used in the output and when looking for the sequence\
      \ of the features.GTF.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--keep_duplicates"
    description: "This flag will disable the default indexing behavior of discarding\
      \ sequence-identical duplicate transcripts. If this flag is passed, then duplicate\
      \ transcripts that appear in the input will be retained and quantified separately.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--keep_fixed_fasta"
    description: "Retain the fixed fasta file (without short transcripts and duplicates,\
      \ clipped, etc.) generated during indexing.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--filter_size"
    alternatives:
    - "-f"
    description: "The size of the Bloom filter that will be used by TwoPaCo during\
      \ indexing. The filter will be of size 2^{filter_size}. The default value of\
      \ -1 means that the filter size will be automatically set based on the number\
      \ of distinct k-mers in the input, as estimated by nthll.\n"
    info: null
    example:
    - -1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--sparse"
    description: "Build the index using a sparse sampling of k-mer positions This\
      \ will require less memory (especially during quantification), but will take\
      \ longer to construct and can slow down mapping / alignment.\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--decoys"
    alternatives:
    - "-d"
    description: "Treat these sequences ids from the reference as the decoys that\
      \ may have sequence homologous to some known transcript. For example in case\
      \ of the genome, provide a list of chromosome names (one per line).\n"
    info: null
    example:
    - "decoys.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_clip"
    description: "Don't clip poly-A tails from the ends of target sequences.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--type"
    alternatives:
    - "-n"
    description: "The type of index to build; the only option is \"puff\" in this\
      \ version of salmon.\n"
    info: null
    example:
    - "puff"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--index"
    alternatives:
    - "-i"
    description: "Salmon index\n"
    info: null
    example:
    - "Salmon_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: "Salmon is a tool for wicked-fast transcript quantification from RNA-seq\
  \ data. It can either make use of pre-computed alignments (in the form of a SAM/BAM\
  \ file) to the transcripts rather than the raw reads, or can be run in the mapping-based\
  \ mode. This component creates a salmon index for the transcriptome to use Salmon\
  \ in the mapping-based mode. It is generally recommend that you build a decoy-aware\
  \ transcriptome file. This is done using the entire genome of the organism as the\
  \ decoy sequence by concatenating the genome to the end of the transcriptome to\
  \ be indexed and populating the decoys.txt file with the chromosome names.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "Transcriptome"
- "Index"
license: "GPL-3.0"
references:
  doi:
  - "10.1038/nmeth.4197"
links:
  repository: "https://github.com/COMBINE-lab/salmon"
  homepage: "https://salmon.readthedocs.io/en/latest/salmon.html"
  documentation: "https://salmon.readthedocs.io/en/latest/salmon.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/salmon:1.10.2--hecfa306_0"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "salmon index -v 2>&1 | sed 's/salmon \\([0-9.]*\\)/salmon: \\1/' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/salmon/salmon_index/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/salmon/salmon_index"
  executable: "target/nextflow/salmon/salmon_index/main.nf"
  viash_version: "0.9.0"
  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g952ff08"
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"
