name: "prepare_genome"
namespace: "workflows"
version: "add_biobase_modules"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--fasta"
    description: "Path to FASTA genome file."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gtf"
    description: "Path to GTF annotation file. This parameter is *mandatory* if --genome\
      \ is not specified."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gff"
    description: "Path to GFF3 annotation file. Required if \"--gtf\" is not specified."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--additional_fasta"
    description: "FASTA file to concatenate to genome FASTA file e.g. containing spike-in\
      \ sequences."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcript_fasta"
    description: "Path to FASTA transcriptome file."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gene_bed"
    description: "Path to BED file containing gene intervals. This will be created\
      \ from the GTF file if not specified."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--splicesites"
    description: "Splice sites file required for HISAT2."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_bbsplit"
    description: "Skip BBSplit for removal of non-reference genome reads."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bbsplit_fasta_list"
    description: "Path to comma-separated file containing a list of reference genomes\
      \ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
      \ be explicitly set to \"false\". The file should contain 2 (comma separated)\
      \ columns - short name and full path to reference genome(s)"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--star_index"
    description: "Path to directory or tar.gz archive for pre-built STAR index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--rsem_index"
    description: "Path to directory or tar.gz archive for pre-built RSEM index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "extra_rsem_prepare_reference_args"
    description: "Extra arguments to pass to rsem-prepare-reference command in addition\
      \ to defaults defined by the pipeline."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--salmon_index"
    description: "Path to directory or tar.gz archive for pre-built Salmon index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--kallisto_index"
    description: "Path to directory or tar.gz archive for pre-built Kallisto index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bbsplit_index"
    description: "Path to directory or tar.gz archive for pre-built BBSplit index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--pseudo_aligner_kmer_size"
    description: "Kmer length passed to indexing step of pseudoaligners."
    info: null
    default:
    - 31
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--gencode"
    description: "Specify if the GTF annotation is in GENCODE format."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--biotype"
    description: "Biotype value to use while appending entries to GTF file when additional\
      \ fasta file is provided."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--filter_gtf"
    description: "Whether to filter the GTF or not?"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--aligner"
    description: "Specifies the alignment algorithm to use - available options are\
      \ 'star_salmon', 'star_rsem' and 'hisat2'."
    info: null
    default:
    - "star_salmon"
    required: false
    choices:
    - "star_salmon"
    - "star_rsem"
    - "hisat2"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--pseudo_aligner"
    description: "Specifies the pseudo aligner to use - available options are 'salmon'.\
      \ Runs in addition to '--aligner'."
    info: null
    default:
    - "salmon"
    required: false
    choices:
    - "salmon"
    - "kallisto"
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--fasta_uncompressed"
    info: null
    default:
    - "reference_genome.fasta"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gtf_uncompressed"
    info: null
    default:
    - "gene_annotation.gtf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcript_fasta_uncompressed"
    info: null
    default:
    - "transcriptome.fasta"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gene_bed_uncompressed"
    info: null
    default:
    - "gene_annotation.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--star_index_uncompressed"
    description: "Path to STAR index."
    info: null
    default:
    - "STAR_index"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--rsem_index_uncompressed"
    description: "Path to directory or tar.gz archive for pre-built RSEM index."
    info: null
    default:
    - "RSEM_index"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--salmon_index_uncompressed"
    description: "Path to Salmon index."
    info: null
    default:
    - "Salmon_index"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--kallisto_index_uncompressed"
    description: "Path to Kallisto index."
    info: null
    default:
    - "Kallisto_index"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bbsplit_index_uncompressed"
    description: "Path to BBSplit index."
    info: null
    default:
    - "BBSplit_index"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--chrom_sizes"
    description: "File containing chromosome lengths"
    info: null
    default:
    - "reference_genome.fasta.sizes"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fai"
    description: "FASTA index file"
    info: null
    default:
    - "reference_genome.fasta.fai"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "nextflow_script"
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
description: "A subworkflow for preparing all the required genome references\n"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
dependencies:
- name: "gunzip"
  repository:
    type: "local"
- name: "gffread"
  repository:
    type: "vsh"
    repo: "biobox"
    tag: "main"
- name: "cat_additional_fasta"
  repository:
    type: "local"
- name: "gtf2bed"
  repository:
    type: "local"
- name: "preprocess_transcripts_fasta"
  repository:
    type: "local"
- name: "gtf_filter"
  repository:
    type: "local"
- name: "rsem/rsem_prepare_reference"
  repository:
    type: "vsh"
    repo: "biobox"
    tag: "main"
- name: "getchromsizes"
  repository:
    type: "local"
- name: "untar"
  repository:
    type: "vsh"
    repo: "craftbox"
    tag: "main"
- name: "star/star_genome_generate"
  repository:
    type: "vsh"
    repo: "biobox"
    tag: "main"
- name: "bbmap_bbsplit"
  repository:
    type: "local"
- name: "salmon/salmon_index"
  repository:
    type: "vsh"
    repo: "biobox"
    tag: "main"
- name: "kallisto/kallisto_index"
  repository:
    type: "local"
repositories:
- type: "vsh"
  name: "biobox"
  repo: "biobox"
  tag: "main"
- type: "vsh"
  name: "craftbox"
  repo: "craftbox"
  tag: "main"
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: "native"
  id: "native"
build_info:
  config: "src/workflows/prepare_genome/config.vsh.yaml"
  runner: "executable"
  engine: "native"
  output: "target/executable/workflows/prepare_genome"
  executable: "target/executable/workflows/prepare_genome/prepare_genome"
  viash_version: "0.9.0"
  git_commit: "b0cbbf82c331a079e3d5ad6df5c8b56388349cac"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/gunzip"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
  - "target/nextflow/cat_additional_fasta"
  - "target/nextflow/gtf2bed"
  - "target/nextflow/preprocess_transcripts_fasta"
  - "target/nextflow/gtf_filter"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference"
  - "target/nextflow/getchromsizes"
  - "target/dependencies/vsh/vsh/craftbox/main/nextflow/untar"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
  - "target/nextflow/bbmap_bbsplit"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
  - "target/nextflow/kallisto/kallisto_index"
package_config:
  version: "add_biobase_modules"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'add_biobase_modules'"
  organization: "vsh"
