def run_cufflinks(data): """Quantitate transcript expression with Cufflinks""" work_bam = data["work_bam"] ref_file = data["sam_ref"] out_dir, fpkm_file = cufflinks.run(work_bam, ref_file, data) data["cufflinks_dir"] = out_dir data["fpkm"] = fpkm_file return [[data]]
def run_cufflinks(data): """Quantitate transcript expression with Cufflinks""" work_bam = dd.get_work_bam(data) ref_file = dd.get_sam_ref(data) out_dir, fpkm_file, fpkm_isoform_file = cufflinks.run(work_bam, ref_file, data) data = dd.set_cufflinks_dir(data, out_dir) data = dd.set_fpkm(data, fpkm_file) data = dd.set_fpkm_isoform(data, fpkm_isoform_file) return [[data]]
def run_cufflinks(data): """Quantitate transcript expression with Cufflinks""" if "cufflinks" in dd.get_tools_off(data): return [[data]] work_bam = dd.get_work_bam(data) ref_file = dd.get_sam_ref(data) out_dir, fpkm_file, fpkm_isoform_file = cufflinks.run( work_bam, ref_file, data) data = dd.set_cufflinks_dir(data, out_dir) data = dd.set_fpkm(data, fpkm_file) data = dd.set_fpkm_isoform(data, fpkm_isoform_file) return [[data]]
def run_cufflinks(data): """Quantitate transcript expression with Cufflinks""" work_bam = data["work_bam"] ref_file = data["sam_ref"] data["cufflinks_dir"] = cufflinks.run(work_bam, ref_file, data) return [[data]]