deseq2.rule.snakefile 1.29 KB
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rule <step_name>__deseq2:
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    input:
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        **<step_name>__deseq2_inputs()
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    output:
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        de_table = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/de_table.csv',
        r_data = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/data.RData',
        PCA = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/PCA_mqc.png',
        Top_genes = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Top_genes_mqc.tsv',
        MA_plot = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/MA_plot_mqc.png',
        Volcano_plot = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Volcano_plot_mqc.png',
        Heatmap = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Heatmap_mqc.png',
    log: config["results_dir"]+'/logs/' + config["<step_name>__deseq2_output_dir"] + '/deseq2_log.txt'
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    params:
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        script = config["<step_name>__deseq2_command"],
        tx2gene = config["<step_name>__deseq2_tx2gene"],
        annotations = config["<step_name>__deseq2_annotations"],
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        outDir = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"],
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        biomaRtDataset = config["<step_name>__deseq2_biomaRtDataset"],
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    script:
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        config["<step_name>__deseq2_script"]