def _maybe_add_junction_files(algorithm, sample, out):
"""
add splice junction files from STAR, if available
"""
junction_bed = dd.get_junction_bed(sample)
if junction_bed:
out.append({
"path": junction_bed,
"type": "bed",
"ext": "SJ",
"dir": "STAR"
})
chimeric_file = dd.get_chimericjunction(sample)
if chimeric_file:
out.append({
"path": chimeric_file,
"type": "tsv",
"ext": "chimericSJ",
"dir": "STAR"
})
sj_file = dd.get_starjunction(sample)
if sj_file:
out.append({
"path": sj_file,
"type": "tab",
"ext": "SJ",
"dir": "STAR"
})
star_summary = dd.get_summary_qc(sample).get("star", None)
if star_summary:
star_log = star_summary["base"]
if star_log:
out.append({"path": star_log, "type": "log", "dir": "STAR"})
return out
def _maybe_add_junction_files(algorithm, sample, out):
"""
add splice junction files from STAR, if available
"""
junction_bed = dd.get_junction_bed(sample)
if junction_bed:
out.append({
"path": junction_bed,
"type": "bed",
"ext": "SJ",
"dir": "STAR"
})
chimeric_file = dd.get_chimericjunction(sample)
if chimeric_file:
out.append({
"path": chimeric_file,
"type": "tsv",
"ext": "chimericSJ",
"dir": "STAR"
})
sj_file = dd.get_starjunction(sample)
if sj_file:
out.append({
"path": sj_file,
"type": "tab",
"ext": "SJ",
"dir": "STAR"
})
return out