def clean_chipseq_alignment(data): aligner = dd.get_aligner(data) assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2." if aligner == "bowtie2": unique_bam = filter_multimappers(dd.get_work_bam(data), data) data["work_bam"] = unique_bam return [[data]] return [[data]]
def clean_chipseq_alignment(data): config = data["config"] aligner = config["algorithm"].get("aligner", None) assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2." if aligner == "bowtie2": work_bam = filter_multimappers(data["work_bam"]) data["work_bam"] = work_bam return [[data]]
def clean_chipseq_alignment(data): aligner = dd.get_aligner(data) data["raw_bam"] = dd.get_work_bam(data) if aligner: assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2." unique_bam = filter_multimappers(dd.get_work_bam(data), data) data["work_bam"] = unique_bam else: logger.info("Warning: When BAM file is given as input, bcbio skips multimappers removal." "If BAM is not cleaned for peak calling, can result in downstream errors.") return [[data]]