openpipeline_qc/src/workflows/generate_qc_report/config.vsh.yaml at f7bdc88ddf2a221000afd2c1e8360f6324f8a8fc · openpipelines-bio/openpipeline_qc · GitHub

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name: generate_qc_report
namespace: workflows
description: Run the ingestion QC report generation
authors:
  - __merge__: /src/authors/jakub_majercik.yaml
    roles: [author]
  - __merge__: /src/authors/dorien_roosen.yaml
    roles: [author]
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [author]
  - __merge__: /src/authors/weiwei_schultz.yaml
    roles: [contributor]
argument_groups:
  # TO DO: it would be nice if the sample metadata was already
  # included in the h5mu files, so that we don't need to pass it.
  - name: Inputs
    arguments:
      - name: --id
        type: string
        required: false
        direction: input
        description: |
          The sample IDs to include in the report. If not provided,
          the sample IDs will be extracted from the h5mu files.
        example: sample1
      - name: --input
        type: file
        required: true
        direction: input
        description: The input h5mu files.
        example: path/to/file1.h5mu
      - name: --ingestion_method
        type: string
        required: true
        choices:
          - cellranger_multi
          - xenium
          - visium
      - name: --sample_metadata
        type: file
        required: false
        direction: input
        description: |
          The sample metadata file corresponding to .obs fields in the h5mu input files, to be used for grouping in the report.
        example: path/to/file.csv
      - name: --max_samples_per_report
        type: integer
        default: 20
        min: 1
        max: 20
        description: |
          The maximum number of samples to be included per report.
          Multiple reports will be generated (with samples equally divided over all reports) if number of input samples exceeds this threshold.
  - name: Options
    arguments:
      - name: "--var_gene_names"
        example: "gene_symbol"
        type: string
        description: |
          The column name in the .var h5mu files that contains the gene names. If not provided, .var_names will be used.
      - name: --obs_metadata
        type: string
        multiple: true
        description: The metadata keys in the h5mu .obs to include in the report.
        example: [donor_id, cell_type, batch, condition]

  - name: QC options
    arguments:
      - name: "--var_name_mitochondrial_genes"
        type: string
        required: false
        default: "mitochondrial"
        description: |
          In which .var slot to store a boolean array corresponding the mitochondrial genes.
      - name: "--var_name_ribosomal_genes"
        type: string
        required: false
        default: "ribosomal"
        description: |
          In which .var slot to store a boolean array corresponding the ribosomal genes.
      - name: --min_total_counts
        type: integer
        description: |
          Minimum total counts for a cell to be included in the output.
        default: 10
        min: 1
      - name: --min_num_nonzero_vars
        type: integer
        description: |
          Minimum number of nonzero vars for a cell to be included in the output.
        default: 10
        min: 1

  - name: Cellbender options
    arguments:
      - name: "--run_cellbender"
        type: boolean
        required: false
        description: Whether to run cellbender or not.
        default: false
      - name: "--cellbender_epochs"
        type: integer
        required: false
        description: Number of epochs to train cellbender.
        default: 150

  - name: Outputs
    arguments:
      - name: --output_qc_report
        type: file
        required: true
        multiple: true
        direction: output
        description: The output HTML report
        example: path/to/file.html
      - name: --output_processed_h5mu
        type: file
        required: true
        direction: output
        description: Folder containing the processed h5mu files.
        default: qc_h5mu

resources:
  - type: nextflow_script
    entrypoint: run_wf
    path: main.nf

test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_no_cellbender
  - type: nextflow_script
    path: test.nf
    entrypoint: test_with_cellbender
  - type: nextflow_script
    path: test.nf
    entrypoint: test_xenium
  - type: nextflow_script
    path: test.nf
    entrypoint: test_visium

dependencies:
  - name: metadata/add_id
    repository: openpipeline
  - name: workflows/qc/qc
    repository: openpipeline
  - name: correction/cellbender_remove_background
    alias: cellbender
    repository: openpipeline
  - name: ingestion_qc/h5mu_to_qc_json
  - name: ingestion_qc/generate_html
  - name: move_files_to_directory
    repository: craftbox

runners:
  - type: nextflow