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