def _update_data(align_file, out_dir, names, data):
data = dd.set_work_bam(data, align_file)
data = dd.set_align_bam(data, align_file)
if dd.get_transcriptome_align(data) and not is_transcriptome_broken(data):
transcriptome_file = _move_transcriptome_file(out_dir, names)
data = dd.set_transcriptome_bam(data, transcriptome_file)
return data
def pipeline_summary(data):
"""Provide summary information on processing sample.
Handles standard and CWL (single QC output) cases.
"""
data = utils.to_single_data(data)
if data["analysis"].startswith("wgbs-seq"):
bismark_bam = dd.get_align_bam(data)
sorted_bam = bam.sort(bismark_bam, data["config"])
data = dd.set_align_bam(data, sorted_bam)
data = dd.set_work_bam(data, bismark_bam)
work_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
if not work_bam or not work_bam.endswith(".bam"):
work_bam = None
if dd.get_ref_file(data):
if work_bam or (tz.get_in(["config", "algorithm", "kraken"],
data)): # kraken doesn't need bam
logger.info("QC: %s %s" % (dd.get_sample_name(data), ", ".join(
dd.get_algorithm_qc(data))))
work_data = cwlutils.unpack_tarballs(utils.deepish_copy(data),
data)
data["summary"] = _run_qc_tools(work_bam, work_data)
if (len(dd.get_algorithm_qc(data)) == 1
and "output_cwl_keys" in data):
data["summary"]["qc"] = data["summary"]["qc"].get(
dd.get_algorithm_qc(data)[0])
return [[data]]
def _update_data(align_file, out_dir, names, data):
data = dd.set_work_bam(data, align_file)
data = dd.set_align_bam(data, align_file)
if dd.get_transcriptome_align(data) and not is_transcriptome_broken():
transcriptome_file = _move_transcriptome_file(out_dir, names)
data = dd.set_transcriptome_bam(data, transcriptome_file)
return data
def _update_data(align_file, out_dir, names, data):
data = dd.set_work_bam(data, align_file)
data = dd.set_align_bam(data, align_file)
transcriptome_file = _move_transcriptome_file(out_dir, names)
data = dd.set_transcriptome_bam(data, transcriptome_file)
sjfile = get_splicejunction_file(out_dir, data)
sjbed = junction2bed(sjfile)
data = dd.set_junction_bed(data, sjbed)
return data
def _update_data(align_file, out_dir, names, data):
data = dd.set_work_bam(data, align_file)
data = dd.set_align_bam(data, align_file)
transcriptome_file = _move_transcriptome_file(out_dir, names)
data = dd.set_transcriptome_bam(data, transcriptome_file)
sjfile = get_splicejunction_file(out_dir, data)
if sjfile:
sjbed = junction2bed(sjfile)
data = dd.set_junction_bed(data, sjbed)
return data
def _update_data(align_file, out_dir, names, data):
data = dd.set_work_bam(data, align_file)
data = dd.set_align_bam(data, align_file)
transcriptome_file = _move_transcriptome_file(out_dir, names)
data = dd.set_transcriptome_bam(data, transcriptome_file)
return data
def _update_data(align_file, out_dir, names, data):
data = dd.set_work_bam(data, align_file)
data = dd.set_align_bam(data, align_file)
transcriptome_file = _move_transcriptome_file(out_dir, names)
data = dd.set_transcriptome_bam(data, transcriptome_file)
return data