chip seq

def _bowtie(workflow, conf):
    for target in conf.sample_targets:
        bowtie = attach_back(workflow,
            ShellCommand(
                "{tool} -p {param[threads]} -S -m {param[max_align]} \
                {param[genome_index]} {input[fastq]} {output[sam]} 2> {output[bowtie_summary]}",
                input={"genome_dir": os.path.dirname(conf.get_path("lib", "genome_index")),
                       "fastq": target + ".fastq"},
                output={"sam": target + ".sam",
                        "bowtie_summary": target + "_bowtie_summary.txt", },
                tool="bowtie",
                param={"threads": 4,
                       "max_align": 1,
                       "genome_index": conf.get_path("lib", "genome_index")}))


        bowtie.update(param=conf.items("bowtie"))
    __sam2bam(workflow, conf)

    ## using bowtie standard error output
    attach_back(workflow,
        PythonCommand(stat_bowtie,
            input={"bowtie_summaries": [t + "_bowtie_summary.txt" for t in conf.sample_targets],
                   "db": ChiLinQC_db,
                   "template": rlang_template},
            output={"json": conf.json_prefix + "_bowtie.json",
                    "R": conf.prefix + "_bowtie.R",
                    "pdf": conf.prefix + "_bowtie.pdf"},
            param={"sams": [t + ".sam" for t in conf.sample_targets], }))