def loadRootJob(self):
"""
Loads the root job in the current job store.
:raises toil.job.JobException: If no root job is set or if the root job doesn't exist in
this job store
:return: The root job.
:rtype: toil.jobGraph.JobGraph
"""
try:
with self.readSharedFileStream(self.rootJobStoreIDFileName) as f:
rootJobStoreID = f.read()
except NoSuchFileException:
raise JobException('No job has been set as the root in this job store')
if not self.exists(rootJobStoreID):
raise JobException("The root job '%s' doesn't exist. Either the Toil workflow "
"is finished or has never been started" % rootJobStoreID)
return self.load(rootJobStoreID)
def scalpel_single(job, config, name, samples, input_bam):
"""Run Scalpel on an an unmatched tumour sample and call somatic variants
:param config: The configuration dictionary.
:type config: dict.
:param sample: sample name.
:type sample: str.
:param input_bam: The input_bam file name to process.
:type input_bam: str.
:returns: str -- The output vcf file name.
"""
cwd = os.getcwd()
output_dir = os.path.join(cwd, "{}-scalpel-output".format(name))
scalpel_vcf = os.path.join(output_dir, "variants.indel.vcf")
fixed_vcf = "{}.scalpel.vcf".format(name)
logfile = "{}.scalpel.log".format(name)
logfile2 = "{}.scalpel_fix.log".format(name)
scalpel_command = [
"{}".format(config['scalpel']['bin']),
"--single",
"--intarget",
# "--covthr",
# "3",
# "--lowcov",
# "1",
"--ref",
"{}".format(config['reference']),
"--bed",
"{}".format(samples[name]['regions']),
"--format",
"vcf",
"--numprocs",
"{}".format(config['scalpel']['num_cores']),
"--bam",
"{}".format(input_bam),
"--dir",
"{}".format(output_dir)
]
fix_sample_name_command = [
"cat", "{}".format(scalpel_vcf), "|", "sed",
"'s/sample/{}/g'".format(name), ">", "{}".format(fixed_vcf)
]
job.fileStore.logToMaster("Scalpel Command: {}\n".format(scalpel_command))
run_and_log_command(" ".join(scalpel_command), logfile)
job.fileStore.logToMaster(
"Scalpel Fix Command: {}\n".format(fix_sample_name_command))
run_and_log_command(" ".join(fix_sample_name_command), logfile2)
file_path = os.path.join(cwd, fixed_vcf)
if os.path.exists(file_path) and os.path.getsize(file_path) > 0:
return scalpel_vcf
else:
job.fileStore.logToMaster(
"Scalpel ran into a problem and no output was generated for file {}. Check logfile"
"{} for details\n".format(scalpel_vcf, logfile))
return JobException(
"Scalpel ran into a problem and no output was generated for file {}. Check logfile"
"{} for details\n".format(scalpel_vcf, logfile))
