def main():
args = parse_args()
synapse_login()
nda_login()
samples = sample_list(args.infile)
for key, val in samples.items():
sample, filetype = key
print(sample)
f_run_info = sample + "/run_info"
run_info(f_run_info)
run_info_append(f_run_info,
"\n#SYNAPSE\nPARENTID={}".format(args.parentid))
jid_list = []
for sdata in val:
fname, loc = sdata
if filetype == "bam":
jid_list.append(submit_pre_jobs_bam(sample, fname, loc))
else:
jid_list.append(submit_pre_jobs_fastq(sample, fname, loc))
jid = ",".join(jid_list)
submit_aln_jobs(sample, jid)
print()
def main():
args = parse_args()
synapse_login()
nda_login()
samples = sample_list(args.infile)
for sample, sdata in samples.items():
print(sample)
run_info(sample + "/run_info")
jid_pre = submit_pre_jobs(sample, sdata)
jid_list = []
for ploidy in range(2, 11):
jid = submit_gatk_jobs(sample, ploidy, jid_pre)
jid = submit_filter_jobs(sample, ploidy, jid)
jid_list.append(jid)
jid = ",".join(jid_list)
submit_post_jobs(sample, jid)
print()
def main():
args = parse_args()
synapse_login()
nda_login()
global down_jid_queue
down_jid_queue = deque([None] * args.con_down_limit)
samples = sample_list(args.sample_list)
for (sample, filetype), sdata in samples.items():
print("- Sample: " + sample)
f_run_jid = sample + "/run_jid"
if q.num_run_jid_in_queue(f_run_jid) > 0:
print("There are submitted jobs for this sample.")
print("Skip to submit jobs.\n")
continue
q.set_run_jid(f_run_jid, new=True)
f_run_info = sample + "/run_info"
run_info(f_run_info)
run_info_append(f_run_info, "\n#RUN_OPTIONS")
run_info_append(f_run_info, "UPLOAD={}".format(args.upload))
run_info_append(f_run_info, "RUN_CNVNATOR={}".format(args.run_cnvnator))
run_info_append(f_run_info, "RUN_MUTECT_SINGLE={}".format(args.run_mutect_single))
if args.run_gatk_hc:
ploidy = " ".join(str(i) for i in args.run_gatk_hc)
run_info_append(f_run_info, "RUN_GATK_HC=True\nPLOIDY=\"{}\"".format(ploidy))
else:
run_info_append(f_run_info, "RUN_GATK_HC={}".format(args.run_gatk_hc))
if filetype == "bam":
jid = submit_pre_jobs_bam(sample, sdata)
else:
jid = submit_pre_jobs_fastq(sample, sdata)
submit_aln_jobs(sample, jid)
print()
def main():
args = parse_args()
synapse_login()
nda_login()
global down_jid_queue
down_jid_queue = deque([None] * args.con_down_limit)
samples = sample_list(args.sample_list)
for (sample, filetype), sdata in samples.items():
print("- Sample: " + sample)
f_run_jid = sample + "/run_jid"
if q.num_run_jid_in_queue(f_run_jid) > 0:
print("There are submitted jobs for this sample.")
print("Skip to submit jobs.\n")
continue
q.set_run_jid(f_run_jid, new=True)
f_run_info = sample + "/run_info"
run_info(f_run_info)
run_info_append(f_run_info, "\n#RUN_OPTIONS")
run_info_append(f_run_info, "UPLOAD={}".format(args.upload))
run_info_append(f_run_info,
"RUN_CNVNATOR={}".format(args.run_cnvnator))
run_info_append(f_run_info,
"RUN_MUTECT_SINGLE={}".format(args.run_mutect_single))
if args.run_gatk_hc:
ploidy = " ".join(str(i) for i in args.run_gatk_hc)
run_info_append(f_run_info,
"RUN_GATK_HC=True\nPLOIDY=\"{}\"".format(ploidy))
else:
run_info_append(f_run_info,
"RUN_GATK_HC={}".format(args.run_gatk_hc))
if filetype == "fastq":
raise Exception("The input filetype should be bam or cram.")
global down_jid
jid_list = []
for fname, loc in sdata:
down_jid = down_jid_queue.popleft()
jid = q.submit(
opt(sample, down_jid),
"{job_home}/pre_1.download.sh {sample} {fname} {loc}".format(
job_home=job_home, sample=sample, fname=fname, loc=loc))
jid_list.append(jid)
down_jid_queue.append(jid)
jid = ",".join(jid_list)
if filetype == "bam":
jid = q.submit(
opt(sample, jid),
"{job_home}/pre_2.bam2cram.sh {sample}".format(
job_home=job_home, sample=sample))
jid = q.submit(
opt(sample, jid),
"{job_home}/pre_2b.unmapped_reads.sh {sample}".format(
job_home=job_home, sample=sample))
jid = q.submit(
opt(sample, jid),
"{job_home}/pre_3.run_variant_calling.sh {sample}".format(
job_home=job_home, sample=sample))
q.submit(
opt(sample, jid),
"{job_home}/pre_4.upload_cram.sh {sample}".format(
job_home=job_home, sample=sample))
print()