integration-workflow-parameters.yaml

project_name: integrated

# comma-separated list of filtered Seurat objects to be integrated

seurat_objects: seurat_1.rds,seurat_2"  

group: "orig.ident"

sample_ids: ""

species: mouse 			# name of species either "mouse" or "human"

results_dir: "./results/"

normalization:
 do_normalization: True
 regress_CC: False
 percent.mito: "percent.mt"
 S_score: "S_score"
 G2M_score: "G2M_score"

integration:
 nfeatures : 3000 		# if "all", union of all genes from all objects will be included
 normalization.method : "SCT"
 reduction: "rpca"  		# options: "cca", "rpca", "jpca", "rlsi"
 dims : 20
 k.anchor : 30

dim_reduction:
 do_PCA: True
 assay: integrated
 n_dims: 20

clustering:
 do_clustering: True
 knn : 20
 resolution: auto


UMAP:
 do_UMAP: True

markers:	
 find_markers : True
 min.pct : 0.25
 logfc.threshold : 0.25
 p_val_adj: 0.05
 top_markers : 5
 GO_enrich: False

output_plots: 
 #generate_plots: False
 reduction: umap # choose name of Seurat's DimReduc object
 assay: RNA
 genesOfinterest_file : "genesOfinterest.txt"
 pointSize : 0.3