intro_text: "MultiQC is a modular tool to aggregate results from bioinformatics analyses across many samples into a single report."
report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/scdownstream/tree/dev" target="_blank">nf-core/scdownstream</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/scdownstream/dev/docs/output" target="_blank">documentation</a>.

custom_content:
  order:
    - Unfiltered_QC_plots
    - Filter_threshold_histograms
    - doublet_predictions
    - Filtered_QC_plots
    - cell_cycle
    - sizes
    - genes_upset
    - scvi
    - scanvi
    - symphony
    - scimilarity
    - pca
    - bbknn
    - combat
    - seurat
    - scanorama
    - expimap
    - scib_metrics_benchmark

report_section_order:
  Unfiltered_QC_plots:
    order: 1000
  Filter_threshold_histograms:
    order: 990
  doublet_predictions:
    order: 980
  Filtered_QC_plots:
    order: 970
  cell_cycle:
    order: 960
  sizes:
    order: 950
  genes_upset:
    order: 940
  scvi:
    order: 920
  scanvi:
    order: 910
  symphony:
    order: 900
  scimilarity:
    order: 890
  pca:
    order: 880
  bbknn:
    order: 870
  combat:
    order: 860
  seurat:
    order: 850
  scanorama:
    order: 840
  expimap:
    order: 830
  scib_metrics_benchmark:
    order: 820
  nf-core-scdownstream-methods-description:
    order: -2001
  multiqc_software_versions:
    order: -2002
  software_versions:
    order: -2002
  nf-core-scdownstream-summary:
    order: -2003

export_plots: true

disable_version_detection: true
