Snakefile 735 Bytes
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__metaphlan2_heatmap_exec_command = config.get('metaphlan2_heatmap', {}).get('exec_command', "metaphlan_hclust_heatmap.py")
__metaphlan2_heatmap_modules = config.get('metaphlan2_heatmap', {}).get('modules')
__metaphlan2_heatmap_options = config.get('metaphlan2_heatmap', {}).get('options', "")
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rule heatmap:
    input:
        __metaphlan2_heatmap_input
    output:
        __metaphlan2_heatmap_output
    params:
        exec_command = __metaphlan2_heatmap_exec_command,
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        modules = __metaphlan2_heatmap_modules,
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        options = __metaphlan2_heatmap_options
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    run:
        if params.modules:
        	shell("module load {params.modules}")
        shell("{params.exec_command} {params.options} --in {input} --out {output}")