add example config and metadata

test/config/Lee2020NatGenet/Lee2020NatGenet_dea_seurat_annotation.csv

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+name,data,assay,metadata,control
+Lee2020NatGenet_cellTypes,test/data/Lee2020NatGenet/object.rds,SCT,cell_type,ALL

test/config/Lee2020NatGenet/Lee2020NatGenet_dea_seurat_config.yaml

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+
+##### RESOURCES #####
+mem: '32000'
+threads: 1 # only DEA rule is multicore and gets 8*threads
+partition: 'shortq'
+
+##### GENERAL #####
+annotation: test/config/Lee2020NatGenet/Lee2020NatGenet_dea_seurat_annotation.csv
+result_path: test/results/Lee2020NatGenet/
+project_name: Lee2020NatGenet
+
+##### DEA #####
+
+# parameters for https://satijalab.org/seurat/reference/findmarkers
+logfc_threshold: 0.1
+test_use: "wilcox"
+min_pct: 0.1
+
+# additional parameter for https://satijalab.org/seurat/reference/findallmarkers
+return_thresh: 1
+
+##### AGGREGATION #####
+# score_formula is used to calculate a score for each gene and comparison (group) that can be used downstream e.g., for preranked GSEA
+# eval based score calculation -> eval(parse(text=" "))
+# DEA result dataframe is called: dea_results
+# available numerical columns: p_val, avg_log2FC, pct.1, pct.2, p_val_adj
+# common/popular example: "-log10(dea_results$p_val)*sign(dea_results$logFC)"
+# if not used leave empty: ""
+score_formula: "-log10(dea_results$p_val)*sign(dea_results$avg_log2FC)"
+
+# filters are applied to the DEA results and used for all outputs
+filters:
+    adj_pval: 0.05
+    lfc: 0.1
+    min_pct: 0.1
+
+##### VISUALIZATION #####
+
+# parameters for https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
+volcano:
+    pCutoff: 0.05
+    FCcutoff: 0.1
+
+# path(s) to feature lists as plain text files (.txt) with one gene per line.
+# used to highlight features in volcano plots and generate LFC clustered heatmaps.
+# only use camelCase for the feature_list names like in the examples below.
+# if not used: put an empty entry e.g., noGenes: ""
+feature_lists:
+    CellTypeMarkers: "test/data/gene_lists/CellTypeMarkers.txt"
+    Epithelial: "test/data/gene_lists/Epithelial.txt"

test/data/gene_lists/CellTypeMarkers.txt

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+KRT19
+EPCAM
+CDH5
+VWF
+COL1A2
+COL1A1
+CD79A
+CD14
+AIF1
+CD3D
+CD2
+PTPRC

test/data/gene_lists/Epithelial.txt

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+EPCAM
+CDH1
+KRT20
+KRT19
+OCLN
+CLDN7
+MUC2
+CEACAM5
+CDX2
+VIL1