input:
  assay: RNA
  umap_reduction: umap.harmony
  seurat_object: /opt/scflowreport_output/intermediate/object_v4compatible.rds
metadata:
  celltypes: ~
  subject_col: ~
  cluster_col: ~
  celltype_col: Annot
  sample_col: orig.ident
  group_col: DISEASES
project:
  species: human
  seed: 1234
  name: Skin
  output_dir: /opt/scflowreport_output
analysis:
  run_overview: no
  run_deg: no
  run_pseudobulk: no
  run_deg_enrichment: no
  run_liana: no
  run_scenic_export: no
  run_scenic_import: no
  run_report: yes
  run_scenic: no
pseudobulk:
  min_cells_per_sample_celltype: 10
  min_samples_per_group: 3
  method: edgeR
  adjusted_p_threshold: 0.05
  log2fc_threshold: 0.25
enrichment:
  run_gprofiler: yes
  run_fgsea: yes
  organism: hsapiens
  min_genes_for_ora: 5
  min_ranked_genes_for_fgsea: 20
  fgsea_collection: H
  fgsea_subcollection: ~
  fgsea_min_size: 15
  fgsea_max_size: 500
  fgsea_eps: 1.0e-10
scenic:
  min_pct_cells_expressed: 0.01
  selected_celltypes: []
  n_workers: 4
  subsample_cells: 0
  diff_auc_threshold: 0.03
  diff_adjusted_p_threshold: 0.05
  enrichment_top_n_targets_per_regulon: 200
  enrichment_importance_quantile: 0.9
  mode: export_then_external_run
  run_per_celltype: yes
  db_dir: /path/to/SCENIC_databases
liana:
  method: natmi
  resource: consensus
  min_cells: 10
  mode: run_per_group
  generate_circos: yes
eligibility:
  min_cells_per_group_celltype_deg: 20
comparison:
  name: AtopicDermatitis vs Control
  group1: ad
  group2: control
deg:
  method: findmarkers
  min_pct: 0.1
  log2fc_threshold: 0.25
  adjusted_p_threshold: 0.05
report:
  title: scFlowReport analysis
  embed_summary_data: yes
  link_full_tables: yes