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- de_log2FoldChange = config["de_log2FoldChange"]
- de_padj = config["de_padj"]
- ExprAnalysis_Dir = config["ExprAnalysis_Dir"]
- rule enrich:
- input:
- config["Annotation_Dir"] + "/anno_stat.txt",
- de = ExprAnalysis_Dir + "/deg/my.gene.counts.matrix.{Case_vs_Control}.DESeq2.DE_results"
- output:
- ExprAnalysis_Dir + "/deg/my.gene.counts.matrix.{Case_vs_Control}.DESeq2.DE_results.ekp_results.txt",
- ExprAnalysis_Dir + "/deg/my.gene.counts.matrix.{Case_vs_Control}.DESeq2.DE_results.ego_results.txt"
- shell:
- "Rscript tools/emcp/enrich.R --orgdb_dir " + config["Annotation_Dir"] + " -d {input.de} --de_log2FoldChange {de_log2FoldChange} --de_padj {de_padj}"
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