def _get_files(data): mapped = bam.mapped(data["work_bam"], data["config"]) in_file = bam.sort(mapped, data["config"], order="queryname") gtf_file = data["genome_resources"]["rnaseq"]["transcripts"] work_dir = data["dirs"].get("work", "work") out_dir = os.path.join(work_dir, "htseq-count") out_file = os.path.join(out_dir, data['rgnames']['sample']) + ".counts" stats_file = os.path.join(out_dir, data['rgnames']['sample']) + ".stats" return in_file, gtf_file, out_file, stats_file
def _get_files(data): mapped = bam.mapped(data["work_bam"], data["config"]) in_file = bam.sort(mapped, data["config"], order="queryname") gtf_file = dd.get_gtf_file(data) work_dir = dd.get_work_dir(data) out_dir = os.path.join(work_dir, "htseq-count") sample_name = dd.get_sample_name(data) out_file = os.path.join(out_dir, sample_name + ".counts") stats_file = os.path.join(out_dir, sample_name + ".stats") return in_file, gtf_file, out_file, stats_file