name: Quantify single nucleus multiome assays using Cell Ranger ARC

description: |
  Using `cellranger-multi` software, barcoded and probe-based libraries for gene expression assays are quantified against an index, which can be optionally created.

tags:
  - 10x
  - quantification
  - rna
  - flex
  - plex
  - antibody derived tags (adt)
  - hashtag oligos (hto)
  - variable diversity joining (vdj)
  - 5' gene expression
  - 3' gene expression

steps:
  # - name: Create missing indexes
  #   description: For datasets that do not have an `index path`, an index is created using the information in the `genome` stanza. The unique set of required indexes are created.
  #   anchor: 28
  #   modules:
  #     - cell_ranger_multi/mkref

  - name: Create anlaysis configuration file
    description: Write a formatted configuration file that includes all libraries in this project which will be subset for libraries in a dataset.
    anchor: 68
    modules:
      - cell_ranger_multi/make_input_csv

  - name: Quantify assays
    description: Use the FastQ files to quantify RNA expression and additional assays in single cells.
    anchor: 119
    modules:
      - cell_ranger_multi/count

output:
  - name: result
    type: channel
    description: A channel of maps that are the same as the input parameter sets but now include `quantification method` and `quantification path` keys.

  - name: tasks
    type: channel
    description: Concatenation of all tasks' parameters and process software versions.

channel tags:
  # - ':genome_indexes.missing': Datasets for which the `index path` is missing; indexes will be created for these.
  # - ':genome_indexes.provided': Datasets for which the `index path` has been provided.
  # - ':index_paths': The indexes that have been created or provided.
  - ':configuration_params': Channel containing information of which samples and assays are in each library.
  - ':libraries_to_quantify': Paths to the newly-created configuration files for each library.
  - ':quantified_datasets': Parameter sets of libraries that were quantified into datasets.
  - ':result': Input parameters with the `index path` (if applicable), `config_file`, `quantification method` and `quantification path` keys added.
  - ':tasks': Each task's output `task.yaml` files from the `task` channel.

parameters:
  # _genome:
  #   - id

  _dataset:
    - adt set path
    - barcode
    - dataset id
    - description
    - fastq paths
    - feature types
    - hto set path
    - index path
    - limsid
    - probe set path
    - vdj index path

authors:
  - "@ChristopherBarrington"