def main():
prefix = os.environ["prefix"]
param_file = os.environ["param_file"]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
assets_uri = os.environ["assets_uri"]
build = os.environ["build"]
in_files = ["{}.sam".format(prefix)]
start_time = datetime.now()
print("SORT SAM for {} was started at {}.".format(prefix, str(start_time)))
task = SDK.Task(step="sort_sam",
prefix=prefix,
in_files=in_files,
param_file=param_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri)
task.get_reference_files(build)
task.download_files("INPUT")
task.download_files("REF")
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print("SORT SAM for {} ended at {}.".format(prefix, str(end_time)))
total_time = end_time - start_time
print("Total time for SORT SAM was {}.".format(str(total_time)))
def main():
prefix = os.environ["prefix"]
param_file = os.environ["param_file"]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
assets_uri = os.environ["assets_uri"]
sample_file = os.environ["sample_file"]
sentieon_pkg = os.environ["sentieon_pkg"]
license_file = os.environ["sentieon_license"]
ome = os.environ["ome"]
build = os.environ["build"]
if ome == "wes":
target_file = os.environ["target_file"]
else:
target_file = None
start_time = datetime.now()
print("Sentieon's GENOTYPER for {} was started at {}.".format(prefix, str(start_time)))
in_files = []
task = SDK.Task(
step="genotyper",
prefix=prefix,
in_files=in_files,
param_file=param_file,
sentieon_pkg=sentieon_pkg,
license_file=license_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri,
target_file=target_file,
sample_file=sample_file)
if ome == "wes" and target_file:
task.download_files("TARGET")
task.get_reference_files(build)
task.get_genotyping_samples()
task.download_files("INPUT")
task.download_files("REF")
task.download_files("SENTIEON")
task.download_files("PARAMS")
# Note: genotyper is the only step where in_files is set as an env variable
# Build in_files from sample_file
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print("Sentieon's GENOTYPER for {} ended at {}.".format(prefix, str(end_time)))
total_time = end_time - start_time
print("Total time for Sentieon's GENOTYPER was {}.".format(str(total_time)))
def main():
prefix = os.environ['prefix']
param_file = os.environ['param_file']
ref_uri = os.environ['ref_uri']
in_uri = os.environ['in_uri']
out_uri = os.environ['out_uri']
assets_uri = os.environ['assets_uri']
build = os.environ['build']
fam_id = os.environ['fam_id']
vcf = '{}.vcf'.format(fam_id)
idx = '{}.idx'.format(vcf)
in_files = [vcf, idx]
print(in_files)
start_time = datetime.now()
print('SCRUB VCF for {} was started at {}.'.format(prefix, str(start_time)))
task = SDK.Task(
step='scrub_vcf',
prefix=prefix,
in_files=in_files,
param_file=param_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri)
dir_contents = os.listdir('.')
print('Current dir contents: {}'.format(str(dir_contents)))
task.get_reference_files(build)
task.download_files('INPUT')
task.download_files('REF')
task.download_files('PARAMS')
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print('SCRUB VCF for {} ended at {}.'.format(prefix, str(end_time)))
total_time = end_time - start_time
print('Total time for SCRUB VCF was {}.'.format(str(total_time)))
def main():
prefix = os.environ["prefix"]
param_file = os.environ["param_file"]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
assets_uri = os.environ["assets_uri"]
build = os.environ["build"]
R1 = os.environ["R1"]
R2 = os.environ["R2"]
in_files = [R1, R2]
threads = os.environ['threads']
print(in_files)
start_time = datetime.now()
print("BWA MEM for {} was started at {}.".format(prefix, str(start_time)))
task = SDK.Task(step="bwa_mem",
prefix=prefix,
threads=threads,
in_files=in_files,
param_file=param_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri)
dir_contents = os.listdir(".")
print("Current dir contents: {}".format(str(dir_contents)))
task.get_reference_files(build)
task.download_files("INPUT")
task.download_files("REF")
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print("BWA MEM for {} ended at {}.".format(prefix, str(end_time)))
total_time = end_time - start_time
print("Total time for BWA MEM was {}.".format(str(total_time)))
def main():
prefix = os.environ["prefix"]
param_file = os.environ["param_file"]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
assets_uri = os.environ["assets_uri"]
vcf = "{}.gt.snp.recal.vcf".format(prefix)
idx = "{}.gt.snp.recal.vcf.idx".format(prefix)
recal_file = "{}.gt.snp.indel.recal.model".format(prefix)
tranches_file = "{}.gt.snp.indel.tranches".format(prefix)
in_files = [vcf, idx, recal_file, tranches_file]
build = os.environ["build"]
start_time = datetime.now()
print("VQSR INDEL APPLY for {} was started at {}.".format(
prefix, str(start_time)))
task = SDK.Task(step="vqsr_indel_apply",
prefix=prefix,
in_files=in_files,
param_file=param_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri)
task.get_reference_files(build)
task.download_files("INPUT")
task.download_files("REF")
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print("VQSR INDEL APPLY for {} ended at {}.".format(prefix, str(end_time)))
total_time = end_time - start_time
print("Total time for VQSR INDEL APPLY was {}.".format(str(total_time)))
def main():
prefix = os.environ["prefix"]
param_file = os.environ["param_file"]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
assets_uri = os.environ["assets_uri"]
build = os.environ["build"]
bam = "{}.sorted.deduped.bam".format(prefix)
bai = "{}.sorted.deduped.bam.bai".format(prefix)
bqsr = "{}.base_recal_table.txt".format(prefix)
in_files = [bam, bai, bqsr]
start_time = datetime.now()
print("BASE RECAL for {} was started at {}.".format(
prefix, str(start_time)))
task = SDK.Task(step="base_recal",
prefix=prefix,
in_files=in_files,
param_file=param_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri)
task.get_reference_files(build)
task.download_files("INPUT")
task.download_files("REF")
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print("BASE RECAL for {} ended at {}.".format(prefix, str(end_time)))
total_time = end_time - start_time
print("Total time for BASE RECAL was {}.".format(str(total_time)))
def main():
prefix = os.environ["prefix"]
param_file = os.environ["param_file"]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
assets_uri = os.environ["assets_uri"]
vcf = "{}.gt.vcf.gz".format(prefix)
tbi = "{}.gt.vcf.gz.tbi".format(prefix)
in_files = [vcf, tbi]
build = os.environ["build"]
start_time = datetime.now()
print("VQSR SNP MODEL for {} was started at {}.".format(
prefix, str(start_time)))
task = SDK.Task(step="vqsr_snp_model",
prefix=prefix,
in_files=in_files,
param_file=param_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri)
task.get_reference_files(build)
task.download_files("INPUT")
task.download_files("REF")
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print("VQSR SNP MODEL for {} ended at {}.".format(prefix, str(end_time)))
total_time = end_time - start_time
print("Total time for VQSR SNP MODEL was {}.".format(str(total_time)))
param_uri = os.environ["param_uri"]
param_file = param_uri.split("/")[-1]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
ref_files = []
in_files = ["{}.sorted.deduped.bam".format(prefix)]
start_time = datetime.now()
print "INDEX BAM for {} was started at {}.".format(prefix, str(start_time))
task = SDK.Task(
step="index_bam",
prefix=prefix,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
raise ValueError(
"Unrecognized build - environment variable mode must be GRCh38 or GRCh37"
)
vcf = "{}.gt.vcf.gz".format(prefix)
tbi = "{}.gt.vcf.gz.tbi".format(prefix)
in_files = [vcf, tbi]
start_time = datetime.now()
print "VQSR SNP MODEL for {} was started at {}.".format(
prefix, str(start_time))
task = SDK.Task(step="vqsr_snp_model",
prefix=prefix,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
)
vcf = "{}.gt.snp.recal.vcf".format(prefix)
idx = "{}.gt.snp.recal.vcf.idx".format(prefix)
recal_file = "{}.gt.snp.indel.recal.model".format(prefix)
tranches_file = "{}.gt.snp.indel.tranches".format(prefix)
in_files = [vcf, idx, recal_file, tranches_file]
start_time = datetime.now()
print "VQSR INDEL APPLY for {} was started at {}.".format(
prefix, str(start_time))
task = SDK.Task(step="vqsr_indel_apply",
prefix=prefix,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
param_uri = os.environ["param_uri"]
param_file = param_uri.split("/")[-1]
ref_uri = os.environ["ref_uri"]
in_uri = os.environ["in_uri"]
out_uri = os.environ["out_uri"]
ref_files = []
in_files = ["{}.sorted.bam".format(prefix)]
start_time = datetime.now()
print "MARK DUPS for {} was started at {}.".format(prefix, str(start_time))
task = SDK.Task(step="mark_dups",
prefix=prefix,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
raise ValueError(
"Unrecognized build - environment variable mode must be GRCh38 or GRCh37"
)
R1 = "{}_R1{}".format(prefix, suffix)
R2 = "{}_R2{}".format(prefix, suffix)
in_files = [R1, R2]
threads = os.environ['threads']
start_time = datetime.now()
print "BWA MEM for {} was started at {}.".format(prefix, str(start_time))
task = SDK.Task(step="bwa_mem",
prefix=prefix,
threads=threads,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri)
dir_contents = os.listdir(".")
print "Current dir contents: {}".format(str(dir_contents))
if not set(in_files).issubset(set(dir_contents)):
task.download_files("INPUT")
if not set(ref_files).issubset(set(dir_contents)):
task.download_files("REF")
if param_file not in dir_contents:
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
"Unrecognized build - environment variable build must be GRCh38 or GRCh37"
)
bam = "{}.sorted.deduped.bam".format(prefix)
bai = "{}.sorted.deduped.bam.bai".format(prefix)
bqsr = "{}.base_recal_table.txt".format(prefix)
in_files = [bam, bai, bqsr]
start_time = datetime.now()
print "BASE RECAL for {} was started at {}.".format(prefix, str(start_time))
task = SDK.Task(step="base_recal",
prefix=prefix,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
raise ValueError("Unrecognized build - environment variable build must be GRCh38 or GRCh37")
if ome == "wes":
target_file = os.environ["target_file"]
ref_files.append(target_file)
else:
target_file = None
start_time = datetime.now()
print "Sentieon's GENOTYPER for {} was started at {}.".format(", ".join(gvcfs), str(start_time))
task = SDK.Task(
step="genotyper",
prefix=prefix,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
sentieon_pkg=sentieon_pkg,
license_file=license_file,
license_uri=license_uri,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
target_file=target_file)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if license_file not in os.listdir("."):
task.download_files("SENTIEON")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
if ome == "wes" and target_file not in os.listdir("."):
def main():
start_point = os.environ['start_point']
prefix = os.environ['prefix']
param_file = os.environ['param_file']
ref_uri = os.environ['ref_uri']
in_uri = os.environ['in_uri']
out_uri = os.environ['out_uri']
assets_uri = os.environ['assets_uri']
sentieon_pkg = os.environ['sentieon_pkg']
license_file = os.environ['sentieon_license']
build = os.environ['build']
ome = os.environ['ome']
if ome == 'wes':
target_file = os.environ['target_file']
else:
target_file = None
if start_point == 'fastq':
bam = '{}.sorted.deduped.recalibrated.bam'.format(prefix)
bai = '{}.sorted.deduped.recalibrated.bai'.format(prefix)
else:
bam = os.environ['in_file']
bai = '{}.bai'.format('.'.join(bam.split('.')[:-1]))
#bai = '{}.bai'.format(bam)
#bai = '{}.crai'.format(bam)
in_files = [bam, bai]
threads = os.environ['threads']
start_time = datetime.now()
print('Sentieons HAPLOTYPER for {} was started at {}.'.format(
prefix, str(start_time)))
task = SDK.Task(step='haplotyper',
prefix=prefix,
threads=threads,
in_files=in_files,
param_file=param_file,
sentieon_pkg=sentieon_pkg,
license_file=license_file,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
assets_uri=assets_uri,
target_file=target_file)
if ome == 'wes' and target_file:
task.download_files('TARGET')
task.get_reference_files(build)
task.download_files('INPUT')
task.download_files('REF')
task.download_files('SENTIEON')
task.download_files('PARAMS')
task.build_cmd()
task.run_cmd()
task.upload_results()
task.cleanup()
end_time = datetime.now()
print('Sentieons HAPLOTYPER for {} ended at {}.'.format(
prefix, str(end_time)))
total_time = end_time - start_time
print('Total time for Sentieons HAPLOTYPER was {}.'.format(
str(total_time)))
else:
target_file = None
bam = "{}.sorted.deduped.bam".format(prefix)
bai = "{}.sorted.deduped.bam.bai".format(prefix)
in_files = [bam, bai]
threads = os.environ['threads']
start_time = datetime.now()
print "BASE RECAL TABLE for {} was started at {}.".format(prefix, str(start_time))
task = SDK.Task(
step="base_recal_table",
prefix=prefix,
threads=threads,
in_files=in_files,
ref_files=ref_files,
param_file=param_file,
param_uri=param_uri,
ref_uri=ref_uri,
in_uri=in_uri,
out_uri=out_uri,
target_file=target_file)
if not set(in_files).issubset(set(os.listdir("."))):
task.download_files("INPUT")
if not set(ref_files).issubset(set(os.listdir("."))):
task.download_files("REF")
if param_file not in os.listdir("."):
task.download_files("PARAMS")
if ome == "wes" and target_file not in os.listdir("."):
task.download_files("TARGET")
task.build_cmd()
task.run_cmd()
