name: "cellranger_multi"
namespace: "mapping"
version: "v4.0.4"
authors:
- name: "Dries Schaumont"
  roles:
  - "maintainer"
  info:
    role: "Core Team Member"
    links:
      email: "dries@data-intuitive.com"
      github: "DriesSchaumont"
      orcid: "0000-0002-4389-0440"
      linkedin: "dries-schaumont"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
- name: "Angela Oliveira Pisco"
  roles:
  - "author"
  info:
    role: "Contributor"
    links:
      github: "aopisco"
      orcid: "0000-0003-0142-2355"
      linkedin: "aopisco"
    organizations:
    - name: "Insitro"
      href: "https://insitro.com"
      role: "Director of Computational Biology"
    - name: "Open Problems"
      href: "https://openproblems.bio"
      role: "Core Member"
- name: "Robrecht Cannoodt"
  roles:
  - "author"
  - "maintainer"
  info:
    role: "Core Team Member"
    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"
- name: "Dries De Maeyer"
  roles:
  - "author"
  info:
    role: "Core Team Member"
    links:
      email: "ddemaeyer@gmail.com"
      github: "ddemaeyer"
      linkedin: "dries-de-maeyer-b46a814"
    organizations:
    - name: "Janssen Pharmaceuticals"
      href: "https://www.janssen.com"
      role: "Principal Scientist"
- name: "Weiwei Schultz"
  roles:
  - "contributor"
  info:
    role: "Contributor"
    organizations:
    - name: "Janssen R&D US"
      role: "Associate Director Data Sciences"
- name: "Dorien Roosen"
  roles:
  - "author"
  info:
    role: "Core Team Member"
    links:
      email: "dorien@data-intuitive.com"
      github: "dorien-er"
      linkedin: "dorien-roosen"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
argument_groups:
- name: "Input files"
  arguments:
  - type: "file"
    name: "--input"
    description: "The FASTQ files to be analyzed. FASTQ files should conform to the\
      \ naming conventions of bcl2fastq and mkfastq:\n`[Sample Name]_S[Sample Index]_L00[Lane\
      \ Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Feature type-specific input files"
  description: "Helper functionality to allow feature type-specific input files, without\
    \ the need to specify\nlibrary_type or library_id. The library_id will be inferred\
    \ from the input paths.\n"
  arguments:
  - type: "file"
    name: "--gex_input"
    description: "The FASTQ files to be analyzed for Gene Expression. FASTQ files\
      \ should conform to the\nnaming conventions of bcl2fastq and mkfastq:\n`[Sample\
      \ Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--abc_input"
    description: "The FASTQ files to be analyzed for Antibody Capture. FASTQ files\
      \ should conform to \nthe naming conventions of bcl2fastq and mkfastq:\n`[Sample\
      \ Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--cgc_input"
    description: "The FASTQ files to be analyzed for CRISPR Guide Capture. FASTQ files\
      \ should conform to\nthe naming conventions of bcl2fastq and mkfastq:\n`[Sample\
      \ Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--mux_input"
    description: "The FASTQ files to be analyzed for Multiplexing Capture. FASTQ files\
      \ should conform to\nthe naming conventions of bcl2fastq and mkfastq:\n`[Sample\
      \ Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--vdj_input"
    description: "The FASTQ files to be analyzed for VDJ. FASTQ files should conform\
      \ to the\nnaming conventions of bcl2fastq and mkfastq:\n`[Sample Name]_S[Sample\
      \ Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--vdj_t_input"
    description: "The FASTQ files to be analyzed for VDJ-T. FASTQ files should conform\
      \ to the naming\nconventions of bcl2fastq and mkfastq:\n`[Sample Name]_S[Sample\
      \ Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--vdj_t_gd_input"
    description: "The FASTQ files to be analyzed for VDJ-T-GD. FASTQ files should\
      \ conform to\nthe naming conventions of bcl2fastq and mkfastq:\n`[Sample Name]_S[Sample\
      \ Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--vdj_b_input"
    description: "The FASTQ files to be analyzed for VDJ-B. FASTQ files should conform\
      \ to\nthe naming conventions of bcl2fastq and mkfastq:\n`[Sample Name]_S[Sample\
      \ Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--agc_input"
    description: "The FASTQ files to be analyzed for Antigen Capture. FASTQ files\
      \ should conform to\nthe naming conventions of bcl2fastq and mkfastq:\n`[Sample\
      \ Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`\n"
    info: null
    example:
    - "mysample_S1_L001_R1_001.fastq.gz"
    - "mysample_S1_L001_R2_001.fastq.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Library arguments"
  arguments:
  - type: "string"
    name: "--library_id"
    description: "The Illumina sample name to analyze. This must exactly match the\
      \ 'Sample Name'part\nof the FASTQ files specified in the `--input` argument.\n"
    info: null
    example:
    - "mysample1"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--library_type"
    description: "The underlying feature type of the library.\n"
    info: null
    example:
    - "Gene Expression"
    required: false
    choices:
    - "Gene Expression"
    - "VDJ"
    - "VDJ-T"
    - "VDJ-B"
    - "VDJ-T-GD"
    - "Antibody Capture"
    - "CRISPR Guide Capture"
    - "Multiplexing Capture"
    - "Antigen Capture"
    - "Custom"
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--library_subsample"
    description: "The rate at which reads from the provided FASTQ files are sampled.\n\
      Must be strictly greater than 0 and less than or equal to 1.\n"
    info: null
    example:
    - "0.5"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--library_lanes"
    description: "Lanes associated with this sample. Defaults to using all lanes."
    info: null
    example:
    - "1-4"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--library_chemistry"
    description: "Only applicable to FRP. Library-specific assay configuration. By\
      \ default,\nthe assay configuration is detected automatically. Typically, users\
      \ will\nnot need to specify a chemistry.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Sample parameters"
  arguments:
  - type: "string"
    name: "--sample_ids"
    alternatives:
    - "--cell_multiplex_sample_id"
    description: "A name to identify a multiplexed sample. Must be alphanumeric with\
      \ hyphens and/or underscores,\nand less than 64 characters. Required for Cell\
      \ Multiplexing libraries.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--sample_description"
    alternatives:
    - "--cell_multiplex_description"
    description: "A description for the sample."
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "integer"
    name: "--sample_expect_cells"
    description: "Expected number of recovered cells, used as input to cell calling\
      \ algorithm.\n"
    info: null
    example:
    - 3000
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "integer"
    name: "--sample_force_cells"
    description: "Force pipeline to use this number of cells, bypassing cell detection.\n"
    info: null
    example:
    - 3000
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Feature Barcode library specific arguments"
  arguments:
  - type: "file"
    name: "--feature_reference"
    description: "Path to the Feature reference CSV file, declaring Feature Barcode\
      \ constructs and associated barcodes.\nRequired only for Antibody Capture or\
      \ CRISPR Guide Capture libraries.\nSee https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref\
      \ for more information.\"\n"
    info: null
    example:
    - "feature_reference.csv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--feature_r1_length"
    description: "Limit the length of the input Read 1 sequence of V(D)J libraries\
      \ to the first N bases,\nwhere N is the user-supplied value. Note that the length\
      \ includes the Barcode and UMI\nsequences so do not set this below 26.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--feature_r2_length"
    description: "Limit the length of the input Read 2 sequence of V(D)J libraries\
      \ to the first N bases,\nwhere N is a user-supplied value. Trimming occurs before\
      \ sequencing metrics are computed\nand therefore, limiting the length of Read\
      \ 2 may affect Q30 scores.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_crispr_umi"
    description: "Set the minimum number of CRISPR guide RNA UMIs required for protospacer\
      \ detection.\nIf a lower or higher sensitivity is desired for detection, this\
      \ value can be customized\naccording to specific experimental needs. Applicable\
      \ only to datasets that include a\nCRISPR Guide Capture library.\n"
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Gene expression arguments"
  description: "Arguments relevant to the analysis of gene expression data."
  arguments:
  - type: "file"
    name: "--gex_reference"
    description: "Genome refence index built by Cell Ranger mkref."
    info: null
    example:
    - "reference_genome.tar.gz"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--gex_secondary_analysis"
    description: "Whether or not to run the secondary analysis e.g. clustering."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--gex_generate_bam"
    description: "Whether to generate a BAM file."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tenx_cloud_token_path"
    description: "The 10x Cloud Analysis user token used to enable cell annotation."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--cell_annotation_model"
    description: "\"Cell annotation model to use. If auto, uses the default model\
      \ for the species.\nIf not given, does not run cell annotation.\"\n"
    info: null
    required: false
    choices:
    - "auto"
    - "human_pca_v1_beta"
    - "mouse_pca_v1_beta"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gex_expect_cells"
    description: "Expected number of recovered cells, used as input to cell calling\
      \ algorithm.\n"
    info: null
    example:
    - 3000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gex_force_cells"
    description: "Force pipeline to use this number of cells, bypassing cell detection.\n"
    info: null
    example:
    - 3000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--gex_include_introns"
    description: "Whether or not to include intronic reads in counts.\nThis option\
      \ does not apply to Fixed RNA Profiling analysis.\n"
    info: null
    default:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gex_r1_length"
    description: "Limit the length of the input Read 1 sequence of V(D)J libraries\
      \ to the first N bases,\nwhere N is the user-supplied value. Note that the length\
      \ includes the Barcode and UMI\nsequences so do not set this below 26.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gex_r2_length"
    description: "Limit the length of the input Read 2 sequence of V(D)J libraries\
      \ to the first N bases,\nwhere N is a user-supplied value. Trimming occurs before\
      \ sequencing metrics are computed\nand therefore, limiting the length of Read\
      \ 2 may affect Q30 scores.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--gex_chemistry"
    description: "Assay configuration. Either specify a single value which will be\
      \ applied to all libraries,\nor a number of values that is equal to the number\
      \ of libararies. The latter is only applicable\nto only applicable to Fixed\
      \ RNA Profiling.\n  - auto: Chemistry autodetection (default)\n  - threeprime:\
      \ Single Cell 3'\n  - SC3Pv1, SC3Pv2, SC3Pv3(-polyA), SC3Pv4(-polyA): Single\
      \ Cell 3' v1, v2, v3, or v4\n  - SC3Pv3HT(-polyA): Single Cell 3' v3.1 HT\n\
      \  - SC-FB: Single Cell Antibody-only 3' v2 or 5'\n  - fiveprime: Single Cell\
      \ 5'\n  - SC5P-PE: Paired-end Single Cell 5'\n  - SC5P-PE-v3: Paired-end Single\
      \ Cell 5' v3\n  - SC5P-R2: R2-only Single Cell 5'\n  - SC5P-R2-v3: R2-only Single\
      \ Cell 5' v3\n  - SCP5-PE-v3: Single Cell 5' paired-end v3 (GEM-X)\n  - SC5PHT\
      \ : Single Cell 5' v2 HT\n  - SFRP: Fixed RNA Profiling (Singleplex)\n  - MFRP:\
      \ Fixed RNA Profiling (Multiplex, Probe Barcode on R2)\n  - MFRP-R1: Fixed RNA\
      \ Profiling (Multiplex, Probe Barcode on R1)\n  - MFRP-RNA: Fixed RNA Profiling\
      \ (Multiplex, RNA, Probe Barcode on R2)\n  - MFRP-Ab: Fixed RNA Profiling (Multiplex,\
      \ Antibody, Probe Barcode at R2:69)\n  - MFRP-Ab-R2pos50: Fixed RNA Profiling\
      \ (Multiplex, Antibody, Probe Barcode at R2:50)\n  - MFRP-RNA-R1: Fixed RNA\
      \ Profiling (Multiplex, RNA, Probe Barcode on R1)\n  - MFRP-Ab-R1: Fixed RNA\
      \ Profiling (Multiplex, Antibody, Probe Barcode on R1)\n  - ARC-v1 for analyzing\
      \ the Gene Expression portion of Multiome data. If Cell Ranger auto-detects\
      \ ARC-v1 chemistry, an error is triggered.\nSee https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry-\
      \ for more information.\n"
    info: null
    default:
    - "auto"
    required: false
    choices:
    - "auto"
    - "threeprime"
    - "fiveprime"
    - "SC3Pv1"
    - "SC3Pv2"
    - "SC3Pv3"
    - "SC3Pv3-polyA"
    - "SC3Pv4"
    - "SC3Pv4-polyA"
    - "SC3Pv3LT"
    - "SC3Pv3HT"
    - "SC3Pv3HT-polyA"
    - "SC5P-PE"
    - "SC5P-PE-v3"
    - "SC5P-R2"
    - "SC-FB"
    - "SC5P-R2-v3"
    - "SCP5-PE-v3"
    - "SC5PHT"
    - "MFRP"
    - "MFRP-R1"
    - "MFRP-RNA"
    - "MFRP-Ab"
    - "SFRP"
    - "MFRP-Ab-R2pos50"
    - "MFRP-RNA-R1"
    - "MFRP-Ab-R1"
    - "ARC-v1"
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "VDJ related parameters"
  arguments:
  - type: "file"
    name: "--vdj_reference"
    description: "VDJ refence index built by Cell Ranger mkref."
    info: null
    example:
    - "reference_vdj.tar.gz"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--vdj_inner_enrichment_primers"
    description: "V(D)J Immune Profiling libraries: if inner enrichment primers other\
      \ than those provided \nin the 10x Genomics kits are used, they need to be specified\
      \ here as a\ntext file with one primer per line.\n"
    info: null
    example:
    - "enrichment_primers.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--vdj_r1_length"
    description: "Limit the length of the input Read 1 sequence of V(D)J libraries\
      \ to the first N bases, where N is the user-supplied value.\nNote that the length\
      \ includes the Barcode and UMI sequences so do not set this below 26.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--vdj_r2_length"
    description: "Limit the length of the input Read 2 sequence of V(D)J libraries\
      \ to the first N bases, where N is a user-supplied value. \nTrimming occurs\
      \ before sequencing metrics are computed and therefore, limiting the length\
      \ of Read 2 may affect Q30 scores\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--vdj_denovo"
    description: "Run in reference-free mode (i.e., do not use annotations). This\
      \ option is not supported for multiplexed experiments.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "3' Cell multiplexing parameters (CellPlex Multiplexing)"
  arguments:
  - type: "string"
    name: "--cell_multiplex_oligo_ids"
    alternatives:
    - "--cmo_ids"
    description: "The Cell Multiplexing oligo IDs used to multiplex this sample. If\
      \ multiple CMOs were used for a sample,\nseparate IDs with a pipe (e.g., CMO301|CMO302).\
      \ Required for Cell Multiplexing libraries.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "double"
    name: "--min_assignment_confidence"
    description: "The minimum estimated likelihood to call a sample as tagged with\
      \ a Cell Multiplexing Oligo (CMO) instead of \"Unassigned\".\nUsers may wish\
      \ to tolerate a higher rate of mis-assignment in order to obtain more singlets\
      \ to include in their analysis,\nor a lower rate of mis-assignment at the cost\
      \ of obtaining fewer singlets.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--cmo_set"
    description: "Path to a custom CMO set CSV file, declaring CMO constructs and\
      \ associated barcodes. If the default CMO reference IDs that are built into\n\
      the Cell Ranger software are required, this option does not need to be used.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--barcode_sample_assignment"
    description: "Path to a barcode-sample assignment CSV file that specifies the\
      \ barcodes that belong to each sample.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Hashtag multiplexing parameters"
  arguments:
  - type: "string"
    name: "--hashtag_ids"
    description: "The hashtag IDs used to multiplex this sample. If multiple antibody\
      \ hashtags were used for the same sample,\nyou can separate IDs with a pipe.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "On-chip multiplexing parameters"
  arguments:
  - type: "string"
    name: "--ocm_barcode_ids"
    description: "The OCM barcode IDs used to multiplex this sample. Must be one of\
      \ OB1, OB2, OB3, OB4.\nIf multiple OCM Barcodes were used for the same sample,\
      \ you can separate IDs\nwith a pipe (e.g., OB1|OB2).\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Flex multiplexing paramaters"
  arguments:
  - type: "file"
    name: "--probe_set"
    description: "A probe set reference CSV file. It specifies the sequences used\
      \ as a reference for probe alignment and the gene ID associated with each probe.\n\
      It must include 4 columns (probe file format 1.0.0): gene_id,probe_seq,probe_id,included,region\
      \ and an optional 5th column (probe file format 1.0.1).\n- gene_id: The Ensembl\
      \ gene identifier targeted by the probe.\n- probe_seq: The nucleotide sequence\
      \ of the probe, which is complementary to the transcript sequence.\n- probe_id:\
      \ The probe identifier, whose format is described in Probe identifiers.\n- included:\
      \ A TRUE or FALSE flag specifying whether the probe is included in the filtered\
      \ counts matrix output or excluded by the probe filter. \n            See filter-probes\
      \ option of cellranger multi. All probes of a gene must be marked TRUE in the\
      \ included column for that gene to be included.\n- region: Present only in v1.0.1\
      \ probe set reference CSV. The gene boundary targeted by the probe. Accepted\
      \ values are spliced or unspliced.\n\nThe file also contains a number of required\
      \ metadata fields in the header in the format #key=value:\n- panel_name: The\
      \ name of the probe set.\n- panel_type: Always predesigned for predesigned probe\
      \ sets.\n- reference_genome: The reference genome build used for probe design.\n\
      - reference_version: The version of the Cell Ranger reference transcriptome\
      \ used for probe design.\n- probe_set_file_format: The version of the probe\
      \ set file format specification that this file conforms to.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--filter_probes"
    description: "If 'false', include all non-deprecated probes listed in the probe\
      \ set reference CSV file.\nIf 'true' or not set, probes that are predicted to\
      \ have off-target activity to homologous genes are excluded from analysis.\n\
      Not filtering will result in UMI counts from all non-deprecated probes,\nincluding\
      \ those with predicted off-target activity, to be used in the analysis.\nProbes\
      \ whose ID is prefixed with DEPRECATED are always excluded from the analysis.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--probe_barcode_ids"
    description: "The Fixed RNA Probe Barcode ID used for this sample, and for multiplex\
      \ GEX + Antibody Capture libraries,\nthe corresponding Antibody Multiplexing\
      \ Barcode IDs. 10x recommends specifying both barcodes (e.g., BC001+AB001)\n\
      when an Antibody Capture library is present. The barcode pair order is BC+AB\
      \ and they\nare separated with a \"+\" (no spaces). Alternatively, you can specify\
      \ the Probe Barcode ID alone and\nCell Ranger's barcode pairing auto-detection\
      \ algorithm will automatically match to the corresponding Antibody\nMultiplexing\
      \ Barcode.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "integer"
    name: "--emptydrops_minimum_umis"
    description: "For singleplex Flex experiments, use this option to adjust the UMI\
      \ cutoff during the second step of cell calling.\nCell Ranger will still perform\
      \ the full cell calling process but will only evaluate barcodes with UMIs above\n\
      the threshold you specify.\n"
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Antigen Capture (BEAM) libary arguments"
  description: "These arguments are recommended if an Antigen Capture (BEAM) library\
    \ is present. \nIt is needed to calculate the antigen specificity score.\n"
  arguments:
  - type: "string"
    name: "--control_id"
    description: "A user-defined ID for any negative controls used in the T/BCR Antigen\
      \ Capture assay. Must match id specified in the feature reference CSV.\nMay\
      \ only include ASCII characters and must not use whitespace, slash, quote, or\
      \ comma characters. \nEach ID must be unique and must not collide with a gene\
      \ identifier from the transcriptome.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--mhc_allele"
    description: "The MHC allele for TCR Antigen Capture libraries. Must match mhc_allele\
      \ name specified in the Feature Reference CSV.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "General arguments"
  description: "These arguments are applicable to all library types.\n"
  arguments:
  - type: "boolean"
    name: "--check_library_compatibility"
    description: "Optional. This option allows users to disable the check that evaluates\
      \ 10x Barcode overlap between\nibraries when multiple libraries are specified\
      \ (e.g., Gene Expression + Antibody Capture). Setting\nthis option to false\
      \ will disable the check across all library combinations. We recommend running\n\
      this check (default), however if the pipeline errors out, users can bypass the\
      \ check to generate\noutputs for troubleshooting.\n"
    info: null
    default:
    - true
    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
    example:
    - "/path/to/output"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Executor arguments"
  arguments:
  - type: "boolean_true"
    name: "--dryrun"
    description: "If true, the output directory will only contain the CWL input files,\
      \ but the pipeline itself will not be executed."
    info: null
    direction: "input"
resources:
- type: "python_script"
  path: "script.py"
  is_executable: true
- type: "file"
  path: "setup_logger.py"
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
description: "Align fastq files using Cell Ranger multi."
test_resources:
- type: "python_script"
  path: "test.py"
  is_executable: true
- type: "file"
  path: "10x_5k_anticmv/raw/"
  dest: "10x_5k_anticmv/raw/"
- type: "file"
  path: "10x_5k_lung_crispr/raw/"
  dest: "10x_5k_lung_crispr/raw/"
- type: "file"
  path: "10x_5k_beam/raw/"
  dest: "10x_5k_beam/raw/"
- type: "file"
  path: "10x_5k_fixed/raw"
  dest: "10x_5k_fixed/raw"
- type: "file"
  path: "raw"
- type: "file"
  path: "reference_gencodev41_chr1"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
license: "MIT"
links:
  repository: "https://github.com/openpipelines-bio/openpipeline"
  docker_registry: "ghcr.io"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
  id: "nextflow"
  directives:
    label:
    - "veryhighmem"
    - "highcpu"
    - "highdisk"
    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"
    script:
    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
engines:
- type: "docker"
  id: "docker"
  image: "quay.io/nf-core/cellranger:10.0.0"
  target_registry: "images.viash-hub.com"
  target_tag: "v4.0.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "procps"
    interactive: false
  - type: "docker"
    run:
    - "cellranger telemetry disable"
  - type: "python"
    user: false
    packages:
    - "pandas"
    - "pyyaml"
    upgrade: true
  test_setup:
  - type: "apt"
    packages:
    - "git"
    interactive: false
  - type: "python"
    user: false
    packages:
    - "viashpy==0.8.0"
    github:
    - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
    upgrade: true
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/mapping/cellranger_multi/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/mapping/cellranger_multi"
  executable: "target/executable/mapping/cellranger_multi/cellranger_multi"
  viash_version: "0.9.4"
  git_commit: "fb7dc76676aa63d06ae1421bbdd6312ad4f67312"
  git_remote: "https://github.com/openpipelines-bio/openpipeline"
package_config:
  name: "openpipeline"
  version: "v4.0.4"
  summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
  description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
    \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
    \nIn terms of workflows, the following has been made available, but keep in mind\
    \ that\nindividual tools and functionality can be executed as standalone components\
    \ as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n\
    \  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample\
    \ processing: cell filtering and doublet detection.\n  * Multisample processing:\
    \ Count transformation, normalization, QC metric calulations.\n  * Integration:\
    \ Clustering, integration and batch correction using single and multimodal methods.\n\
    \  * Downstream analysis workflows\n"
  info:
    test_resources:
    - type: "s3"
      path: "s3://openpipelines-data"
      dest: "resources_test"
    nextflow_labels_ci:
    - path: "src/workflows/utils/labels_ci.config"
      description: "Adds the correct memory and CPU labels when running on the Viash\
        \ Hub CI."
  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'v4.0.4'"
  keywords:
  - "single-cell"
  - "multimodal"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/openpipelines-bio/openpipeline"
    docker_registry: "ghcr.io"
    homepage: "https://openpipelines.bio"
    documentation: "https://openpipelines.bio/fundamentals"
    issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
