def main():
args = parse_args()
q = GridEngineQueue()
jid_list = []
for pu in [fastq.split(".")[1] for fastq in glob.glob("{sample}/fastq/{sample}.*.R1.fastq.gz".format(sample=args.sample))]:
jid_list.append(q.submit(opt(args.sample),
"{job_home}/aln_1.align_sort.sh {sample} {pu}".format(job_home=job_home, sample=args.sample, pu=pu)))
jid = ",".join(jid_list)
jid = q.submit(opt(args.sample, jid),
"{job_home}/aln_2.merge_bam.sh {sample}".format(job_home=job_home, sample=args.sample))
jid = q.submit(opt(args.sample, jid),
"{job_home}/aln_3.markdup.sh {sample}".format(job_home=job_home, sample=args.sample))
jid = q.submit(opt(args.sample, jid),
"{job_home}/aln_4.indel_realign.sh {sample}".format(job_home=job_home, sample=args.sample))
jid = q.submit(opt(args.sample, jid),
"{job_home}/aln_5.bqsr.sh {sample}".format(job_home=job_home, sample=args.sample))
if parentid(args.sample) != "None":
q.submit(opt(args.sample, jid),
"{job_home}/aln_6.upload_bam.sh {sample}".format(job_home=job_home, sample=args.sample))
import argparse
import os
import sys
from collections import defaultdict
cmd_home = os.path.dirname(os.path.realpath(__file__))
pipe_home = os.path.normpath(cmd_home + "/..")
job_home = cmd_home + "/job_scripts"
sys.path.append(pipe_home)
from library.config import run_info, log_dir
from library.login import synapse_login, nda_login
from library.parser import sample_list
from library.job_queue import GridEngineQueue
q = GridEngineQueue()
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)
def main():
args = parse_args()
q = GridEngineQueue()
q.set_run_jid(args.sample_name + "/run_jid")
jid_list = []
fastq_path = "{sample}/fastq/{sample}.*.R1.fastq.gz".format(
sample=args.sample_name)
done_path = "{sample}/run_status/aln_1.align_sort.*.done".format(
sample=args.sample_name)
pu_list = set([
fastq.replace(".R1.fastq.gz", "").split(".")[-1]
for fastq in glob.glob(fastq_path)
] + [done.split(".")[-2] for done in glob.glob(done_path)])
for pu in pu_list:
jid_list.append(
q.submit(
opt(args.sample_name),
"{job_home}/aln_1.align_sort.sh {sample} {pu}".format(
job_home=job_home, sample=args.sample_name, pu=pu)))
jid = ",".join(jid_list)
jid = q.submit(
opt(args.sample_name, jid),
"{job_home}/aln_2.merge_bam.sh {sample}".format(
job_home=job_home, sample=args.sample_name))
jid = q.submit(
opt(args.sample_name, jid),
"{job_home}/aln_3.markdup.sh {sample}".format(job_home=job_home,
sample=args.sample_name))
jid = q.submit(
opt(args.sample_name, jid),
"{job_home}/aln_4.indel_realign.sh {sample}".format(
job_home=job_home, sample=args.sample_name))
jid = q.submit(
opt(args.sample_name, jid),
"{job_home}/aln_5.bqsr.sh {sample}".format(job_home=job_home,
sample=args.sample_name))
aln_jid = jid
jid = q.submit(
opt(args.sample_name, aln_jid),
"{job_home}/post_1.unmapped_reads.sh {sample}".format(
job_home=job_home, sample=args.sample_name))
save_hold_jid(
"{sample}/alignment/hold_jid".format(sample=args.sample_name), jid)
jid = q.submit(
opt(args.sample_name, aln_jid),
"{job_home}/post_2.run_variant_calling.sh {sample}".format(
job_home=job_home, sample=args.sample_name))
q.submit(
opt(args.sample_name, jid),
"{job_home}/post_3.upload_cram.sh {sample}".format(
job_home=job_home, sample=args.sample_name))