name: "prot_multisample"
namespace: "workflows/prot"
scope: "public"
description: "Processing unimodal multi-sample ADT data."
info:
  image: /images/concepts/fig_workflow_multiomics_adt_multisample.svg
  test_dependencies:
authors:
  - __merge__: /src/authors/dries_schaumont.yaml
    roles: [ author ]
argument_groups:
  - name: "Inputs"
    arguments:
      - name: "--id"
        required: true
        type: string
        description: ID of the concatenated file
        example: concatenated
      - name: "--input"
        required: true
        type: file
        description: Path to the samples.
        example: dataset.h5mu
      - name: "--layer"
        type: string
        description: "Input layer to use. If not specified, .X is used."
  - name: "Outputs"
    arguments:
      - name: "--output"
        type: file
        required: true
        direction: output
        description: Destination path to the output.
        example: output.h5mu
  - name: "QC metrics calculation options"
    arguments:
      - name: "--var_qc_metrics"
        description: |
          Keys to select a boolean (containing only True or False) column from .var.
          For each cell, calculate the proportion of total values for genes which are labeled 'True', 
          compared to the total sum of the values for all genes. Defaults to the value from
          --var_name_mitochondrial_genes.
        type: string
        multiple: True
        multiple_sep: ','
        required: false
        example: "ercc,highly_variable"
      - name: "--top_n_vars"
        type: integer
        description: |
          Number of top vars to be used to calculate cumulative proportions.
          If not specified, proportions are not calculated. `--top_n_vars 20,50` finds
          cumulative proportion to the 20th and 50th most expressed vars.
        multiple: true
        multiple_sep: ','
        required: false
        default: [50, 100, 200, 500]
      - name: "--output_obs_num_nonzero_vars"
        description: |
          Name of column in .obs describing, for each observation, the number of stored values
          (including explicit zeroes). In other words, the name of the column that counts
          for each row the number of columns that contain data.
        type: string
        required: false
        default: "num_nonzero_vars"
      - name: "--output_obs_total_counts_vars"
        description: |
          Name of the column for .obs describing, for each observation (row),
          the sum of the stored values in the columns.
        type: string
        required: false
        default: total_counts
      - name: "--output_var_num_nonzero_obs"
        description: |
          Name of column describing, for each feature, the number of stored values
          (including explicit zeroes). In other words, the name of the column that counts
          for each column the number of rows that contain data.
        type: string
        required: false
        default: "num_nonzero_obs"
      - name: "--output_var_total_counts_obs"
        description: |
          Name of the column in .var describing, for each feature (column),
          the sum of the stored values in the rows.
        type: string
        required: false
        default: total_counts
      - name: "--output_var_obs_mean"
        type: string
        description: |
          Name of the column in .obs providing the mean of the values in each row.
        default: "obs_mean"
        required: false
      - name: "--output_var_pct_dropout"
        type: string
        default: "pct_dropout"
        description: |
          Name of the column in .obs providing for each feature the percentage of
          observations the feature does not appear on (i.e. is missing). Same as `--output_var_num_nonzero_obs`
          but percentage based.
  - name: "CLR arguments"
    arguments:
      - name: "--clr_axis"
        type: integer
        description: Axis across which CLR is performed.
        default: 0
        required: false
dependencies:
  - name: transform/clr
  - name: workflows/qc/qc
    alias: prot_qc
resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf
  - type: file
    path: /src/workflows/utils/
test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf
  - path: /resources_test/pbmc_1k_protein_v3
runners:
  - type: nextflow