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]]
