config.yaml

#These are also default settings of a Cellsnake run without any configfile
#basic paramaters
min_cells: 3 #seurat defaults, recommended
min_features: 200 #seurat defaults, recommended, nFeature_RNA
max_features: Inf #seurat default, nFeature_RNA, 5000 can be a good cutoff
max_molecules: Inf #seurat default, nCount_RNA, to filter potential doublets, doublet filtering is already default, so keep this Inf
min_molecules: 0 #seurat default, nCount_RNA, min_features usually handles this so keep it 0


percent_mt: 10 #Mitochondrial genes maximum percentage (0-100), default 10, you can use "auto"
percent_rp: 0 #Ribosomal genes minimum percentage (0-100), default no filtering
highly_variable_features: 2000 #seurat defaults, recommended
variable_selection_method: "vst" #seurat defaults, recommended

#plotting paramaters
min_percentage_to_plot: 2 #only plot clusters with more than 2% of cells, still all of them visible on HTMLs and on plots if labels are True
show_labels: T #show labels on plots

#doublet filtering, True:T or False:F
doublet_filter: T #this may fail on some samples

#clustering and normalization paramaters
normalization_method: "LogNormalize"
scale_factor: 10000
resolution: "0.8" #seurat default

#Differential expression paramaters
logfc_threshold: 0.25
test_use: "wilcox"
marker_plots_per_cluster_n: 20 #plot summary marker plots for top markers
umap_markers_plot: True
tsne_markers_plot: False

#enrichment paramaters
mapping: "org.Hs.eg.db" #you may install others from Bioconductor, this is for human
organism: "hsa" #alternatives https://www.genome.jp/kegg/catalog/org_list.html

#SingleR reference
singler_ref: "BlueprintEncodeData" # https://bioconductor.org/packages/release/data/experiment/vignettes/celldex/inst/doc/userguide.html#1_Overview
singler_granulation: "label.main" #label.main or label.fine

#celltypist
celltypist_model: "Immune_All_Low.pkl" #refer to Celltypist for another model 

#krakendb settings
kraken_db_folder:
taxa: "genus" # available options "domain", "kingdom", "phylum", "class", "order", "family", "genus", "species"
microbiome_min_cells: 1
microbiome_min_features: 3
confidence: 0.05 #see kraken2 manual
min_hit_groups: 4 #see kraken2 manual

#cellchat
species: "human" #human or mouse is accepted, http://www.cellchat.org/cellchatdb/

#integration params
dims: 30
reduction: "cca"