htseq_count.rule.snakefile 836 Bytes
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rule <step_name>__htseq_count:
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    input:
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        **<step_name>__htseq_count_inputs()
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    output:
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        stats = config["results_dir"]+'/' + config["<step_name>__htseq_count_output_dir"] + '/{sample}.txt',
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    log:
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        config["results_dir"]+'/logs/' + config["<step_name>__htseq_count_output_dir"] + '/{sample}_htseq_count_log.txt'
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    params:
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        command = config["<step_name>__htseq_count_command"],
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        htseq_count_minaqual = config["<step_name>__htseq_count_minaqual"],
        htseq_stranded = config["<step_name>__htseq_stranded"],
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        output_dir = config["results_dir"]+'/'+config["<step_name>__htseq_count_output_dir"]
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    shell:
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        "{params.command} -f bam -a  {params.htseq_count_minaqual}  -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2> {log} > {output.stats}"