name: "cellranger_count"
namespace: "cellranger"
version: "main"
authors:
- name: "Emma Rousseau"
  roles:
  - "author"
  info:
    links:
      github: "emmarousseau"
      linkedin: "emmarousseau1"
- name: "Robrecht Cannoodt"
  roles:
  - "author"
  info:
    links:
      email: "robrecht@data-intuitive.com"
      github: "rcannood"
      orcid: "0000-0003-3641-729X"
      linkedin: "robrechtcannoodt"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Science Engineer"
    - name: "Open Problems"
      href: "https://openproblems.bio"
      role: "Core Member"
argument_groups:
- name: "FASTQ inputs"
  arguments:
  - type: "file"
    name: "--fastqs"
    description: "The fastq.gz files to align. Can also be a single directory containing\
      \ fastq.gz files."
    info: null
    example:
    - "sample_S1_L001_R1_001.fastq.gz"
    - "sample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--description"
    description: "Sample description to embed in output files"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sample"
    description: "Prefix of the filenames of FASTQs to select"
    info: null
    example:
    - "sample_S1"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--lanes"
    description: "Only use FASTQs from selected lanes."
    info: null
    example:
    - 1
    - 2
    - 3
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--libraries"
    description: "CSV file declaring input library data sources"
    info: null
    example:
    - "libraries.csv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Reference inputs"
  arguments:
  - type: "file"
    name: "--transcriptome"
    description: "Path of folder containing 10x-compatible transcriptome reference.\
      \ Can also be a `.tar.gz` file."
    info: null
    example:
    - "transcriptome.tar.gz"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--feature_ref"
    description: "Feature reference CSV file, declaring Feature Barcode constructs\
      \ and associated barcodes"
    info: null
    example:
    - "feature_ref.csv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Analysis settings"
  arguments:
  - type: "integer"
    name: "--expect_cells"
    description: "Expected number of recovered cells, used as input to cell calling\
      \ algorithm."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--force_cells"
    description: "Force pipeline to use this number of cells, bypassing cell calling\
      \ algorithm. Minimum: 10.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--r1_length"
    description: "Hard trim the input Read 1 to this length before analysis"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--r2_length"
    description: "Hard trim the input Read 2 to this length before analysis"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--include_introns"
    description: "Include intronic reads in count. Default: true."
    info: null
    direction: "input"
  - type: "string"
    name: "--chemistry"
    description: "Assay configuration.\n\nNOTE: by default the assay configuration\
      \ is detected automatically, which is the recommended mode. You usually will\
      \ not need to specify a chemistry. \n\nOptions are:\n\n- `'auto'` for autodetection\n\
      - `'threeprime'` for Single Cell 3'\n- `'fiveprime'` for Single Cell 5'\n- `'SC3Pv1'`\
      \ or `'SC3Pv2'` or `'SC3Pv3'` or `'SC3Pv4'` for\nSingle Cell 3' v1/v2/v3/v4\n\
      - `'SC3Pv3LT'` for Single Cell 3' v3 LT\n- `'SC3Pv3HT'` for Single Cell 3' v3\
      \ HT\n- `'SC5P-PE'` or `'SC5P-PE-v3'` or `'SC5P-R2'` or `'SC5P-R2-v3'` for Single\
      \ Cell 5', paired-end/R2-only\n- `'SC-FB'` for Single Cell Antibody-only 3'\
      \ v2 or 5'\n\nTo analyze the GEX portion of multiome data, chemistry must be\
      \ set to `'ARC-v1'`.\n\nSee the [10x Genomics FAQ](https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry-)\
      \ for more information on how chemistry is detected.\n"
    info: null
    example:
    - "auto"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--cell_annotation_model"
    description: "Cell annotation model to use. Valid model names can be viewed by\n\
      running `cellranger cloud annotation models` or on the\n[10x Genomics Support\
      \ site](https://www.10xgenomics.com/support).\n\nIf \"auto\", uses the default\
      \ model for the species.\nIf not provided, does not run cell annotation.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_crispr_umi"
    description: "Minimum CRISPR UMI threshold. Default: 3.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "The folder to store the alignment results."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--create_bam"
    description: "Enable or disable BAM file generation. Setting this to false\nreduces\
      \ the total computation time and the size of the output\ndirectory (BAM file\
      \ not generated). We recommend setting\nit to true if unsure. See https://10xgen.com/create-bam\
      \ for\nadditional guidance.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_secondary"
    description: "Disable secondary analysis, e.g. clustering."
    info: null
    direction: "input"
- name: "Additional arguments"
  arguments:
  - type: "boolean_true"
    name: "--no_libraries"
    description: "Proceed with processing using a `--feature_ref` but no Feature Barcode\
      \ libraries specified with the 'libraries' flag.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--check_library_compatibility"
    description: "Whether to check for barcode compatibility between libraries.\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--tenx_cloud_token"
    description: "The path to the 10x Cloud Analysis user token used to enable cell\n\
      annotation. If not provided, will default to the location stored\nthrough cellranger\
      \ cloud auth setup.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--dry"
    description: "Do not execute the pipeline. Generate a pipeline invocation (.mro)\
      \ file and stop.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
summary: "Align fastq files using Cell Ranger count."
description: "Count gene expression and/or feature barcode reads from a single sample\
  \ and GEM well\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "cellranger"
  - "ps"
keywords:
- "cellranger"
- "single-cell"
- "rna-seq"
- "alignment"
- "count"
license: "Proprietary"
references:
  doi:
  - "10.1038/ncomms14049"
links:
  repository: "https://github.com/10XGenomics/cellranger/blob/main/bin/sc_rna/count"
  homepage: "https://www.10xgenomics.com/support/software/cell-ranger/latest"
  documentation: "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count"
  issue_tracker: "https://github.com/10XGenomics/cellranger/issues"
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/nf-core/cellranger:8.0.0"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "DEBIAN_FRONTEND=noninteractive apt update && \\\napt upgrade -y && apt install\
      \ -y procps && rm -rf /var/lib/apt/lists/*\n"
  - type: "docker"
    run:
    - "cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/cellranger/cellranger_count/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/cellranger/cellranger_count"
  executable: "target/nextflow/cellranger/cellranger_count/main.nf"
  viash_version: "0.9.4"
  git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b"
  git_remote: "https://github.com/viash-hub/biobox"
package_config:
  name: "biobox"
  version: "main"
  summary: "A curated collection of high-quality, standalone bioinformatics components\
    \ built with [Viash](https://viash.io).\n"
  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
    \ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
    \ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
    \ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
    \ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
    \ Run components directly via the command line or seamlessly integrate them into\
    \ Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
    \ for components and parameters.\n    * Full exposure of underlying tool arguments.\n\
    \    * Containerized (Docker) for dependency management and reproducibility.\n\
    \    * Unit tested for verified functionality.\n"
  info: null
  viash_version: "0.9.4"
  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"
