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Progress to merge #8

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dc865c7
adding recent changes
Oct 18, 2024
f2914be
pushing recent edits
Jan 14, 2025
2b17a71
adding recent changes
Feb 12, 2025
6d13d9f
adding recent changes
Apr 15, 2025
d003f3c
adding changes
Sep 4, 2025
0b1abcb
fixing enhancer TF enrichment file path to create summary Excel sheet
Nov 24, 2025
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1 change: 1 addition & 0 deletions config/config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
"sampleName": "IGVF_b01_LeftCortex",
"celltype": "brain",
"organism": "mouse",
"technology": "10x",
"cNMF_gene_selection": ["top2000VariableGenes", "all_genes"],
"Perturb-seq": "False",
"num_Genes_per_MAST_runGroup": 20,
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9 changes: 5 additions & 4 deletions workflow/Snakefile
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Expand Up @@ -21,6 +21,7 @@ include: "rules/program_prioritization.smk"
if config["Perturb-seq"] == "True":
include: "rules/cNMF_Perturb-seq_analysis.smk"

# Need to add back for the overall pipeline (250113)
if not os.path.isfile(config["fimo_formatted"]):
include: "rules/match_motifs.smk"

Expand All @@ -47,7 +48,7 @@ def get_output_files(wildcards):
Var_k_summary_txt = expand(os.path.join(config["analysisDir"],"{folder}/{sample}/K{k}/threshold_{threshold}/summary.varianceExplained.df.txt"), folder = config["cNMF_gene_selection"], sample=config["sampleName"], k=config["k"], threshold=[n.replace(".","_") for n in config["thresholds"]]),

## motif enrichment preparation
fimo_result = expand(os.path.join(config["analysisDir"], "{folder}/{sample}/fimo/fimo_out/fimo.txt"), folder = config["cNMF_gene_selection"], sample=config["sampleName"]),
fimo_result = expand(os.path.join(config["analysisDir"], "{folder}/{sample}/fimo/fimo_out/fimo.tsv"), folder = config["cNMF_gene_selection"], sample=config["sampleName"]),

## main results
cNMF_Results = expand(os.path.join(config["analysisDir"], "{folder}/{sample}/K{k}/threshold_{threshold}/cNMF_results.k_{k}.dt_{threshold}.RData"), folder = config["cNMF_gene_selection"], sample=config["sampleName"], k=config["k"], threshold=[n.replace(".","_") for n in config["thresholds"]]),
Expand All @@ -66,7 +67,7 @@ def get_output_files(wildcards):
gsea_clusterProfiler_plot = expand(os.path.join(config["figDir"], "{folder}/{sample}/K{k}/{sample}_K{k}_dt_{threshold}_top10EnrichedPathways_GeneRankingType{ranking_type}_EnrichmentType{GSEA_type}.pdf"), folder = config["cNMF_gene_selection"], sample=config["sampleName"], k=config["k"], threshold=[n.replace(".","_") for n in config["thresholds"]], ranking_type = ["zscore", "raw", "median_spectra", "median_spectra_zscore"], GSEA_type = ["GOEnrichment", "PosGenesGOEnrichment", "ByWeightGSEA", "GSEA"]),

## Program Summary Table
ProgramSummary = expand(os.path.join(config["analysisDir"], "{folder}/{sample}/K{k}/threshold_{threshold}/{sample}_ProgramSummary_k_{k}.dt_{threshold}.txt"), folder = config["cNMF_gene_selection"], sample=config["sampleName"], k=config["k"], threshold=[n.replace(".","_") for n in config["thresholds"]]),
ProgramSummary = expand(os.path.join(config["analysisDir"], "{folder}/{sample}/K{k}/threshold_{threshold}/{sample}_ProgramSummary_k_{k}.dt_{threshold}.xlsx"), folder = config["cNMF_gene_selection"], sample=config["sampleName"], k=config["k"], threshold=[n.replace(".","_") for n in config["thresholds"]]),
ComprehensiveProgramSummary = expand(os.path.join(config["analysisDir"], "{folder}/{sample}/K{k}/threshold_{threshold}/{sample}_k_{k}.dt_{threshold}_ComprehensiveProgramSummary.xlsx"), folder = config["cNMF_gene_selection"], sample=config["sampleName"], k=config["k"], threshold=[n.replace(".","_") for n in config["thresholds"]]),

## PoPS
Expand Down Expand Up @@ -109,8 +110,8 @@ def get_output_files(wildcards):
output_files.extend(list(clusterProfiler_result)) ## rule: clusterProfiler_GSEA, across K plots
output_files.extend(list(GSEA_plots))
output_files.extend(list(TFMotifEnrichment_plots))
output_files.extend(list(model_yaml))
output_files.extend(list(cellxgene_h5ad))
# output_files.extend(list(model_yaml))
# output_files.extend(list(cellxgene_h5ad))
output_files.extend(list(ProgramSummary))
output_files.extend(list(ComprehensiveProgramSummary))
# output_files.extend(list(clusterProfiler_top300Gene_GO_result))
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