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 = 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
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
