def merge_sample(data):
"""Merge fastq and BAM files for multiple samples.
"""
logger.info("Combining fastq and BAM files %s" % str(data["name"]))
config = shared.update_config_w_custom(data["config"], data["info"])
genome_build, sam_ref = shared.ref_genome_info(data["info"], config,
data["dirs"])
if config["algorithm"].get("upload_fastq", False):
fastq1, fastq2 = combine_fastq_files(data["fastq_files"],
data["dirs"]["work"], config)
else:
fastq1, fastq2 = None, None
sort_bam = merge_bam_files(data["bam_files"], data["dirs"]["work"], config)
return [[{
"name": data["name"],
"metadata": data["info"].get("metadata", {}),
"info": data["info"],
"genome_build": genome_build,
"sam_ref": sam_ref,
"work_bam": sort_bam,
"fastq1": fastq1,
"fastq2": fastq2,
"dirs": data["dirs"],
"config": config,
"config_file": data["config_file"]
}]]
def merge_sample(data):
"""Merge fastq and BAM files for multiple samples.
"""
logger.info("Combining fastq and BAM files %s" % str(data["name"]))
config = _update_config_w_custom(data["config"], data["info"])
genome_build, sam_ref = ref_genome_info(data["info"], config, data["dirs"])
fastq1, fastq2 = combine_fastq_files(data["fastq_files"], data["dirs"]["work"],
config)
sort_bam = merge_bam_files(data["bam_files"], data["dirs"]["work"], config)
return [[{"name": data["name"],
"genome_build": genome_build, "sam_ref": sam_ref,
"work_bam": sort_bam, "fastq1": fastq1, "fastq2": fastq2,
"dirs": data["dirs"], "config": config,
"config_file": data["config_file"]}]]
def merge_sample(data):
"""Merge fastq and BAM files for multiple samples.
"""
logger.info("Combining fastq and BAM files %s" % str(data["name"]))
config = _update_config_w_custom(data["config"], data["info"])
genome_build, sam_ref = ref_genome_info(data["info"], config, data["dirs"])
if config["algorithm"].get("upload_fastq", False):
fastq1, fastq2 = combine_fastq_files(data["fastq_files"], data["dirs"]["work"],
config)
else:
fastq1, fastq2 = None, None
sort_bam = merge_bam_files(data["bam_files"], data["dirs"]["work"], config)
return [[{"name": data["name"], "metadata": data["info"].get("metadata", {}),
"genome_build": genome_build, "sam_ref": sam_ref,
"work_bam": sort_bam, "fastq1": fastq1, "fastq2": fastq2,
"dirs": data["dirs"], "config": config,
"config_file": data["config_file"]}]]
def merge_sample(data):
"""Merge fastq and BAM files for multiple samples.
"""
logger.info("Combining fastq and BAM files %s" % str(data["name"]))
config = _update_config_w_custom(data["config"], data["info"])
genome_build, sam_ref = ref_genome_info(data["info"], config, data["dirs"])
fastq1, fastq2 = combine_fastq_files(data["fastq_files"],
data["dirs"]["work"], config)
sort_bam = merge_bam_files(data["bam_files"], data["dirs"]["work"], config)
return [[{
"name": data["name"],
"genome_build": genome_build,
"sam_ref": sam_ref,
"work_bam": sort_bam,
"fastq1": fastq1,
"fastq2": fastq2,
"dirs": data["dirs"],
"config": config,
"config_file": data["config_file"]
}]]
def merge_sample(data):
"""Merge fastq and BAM files for multiple samples.
"""
logger.debug("Combining fastq and BAM files %s" % str(data["name"]))
config = config_utils.update_w_custom(data["config"], data["info"])
config = config_utils.add_cached_versions(config)
genome_build, sam_ref = shared.ref_genome_info(data["info"], config, data["dirs"])
if config["algorithm"].get("upload_fastq", False):
fastq1, fastq2 = combine_fastq_files(data["fastq_files"], data["dirs"]["work"],
config)
else:
fastq1, fastq2 = None, None
out_file = os.path.join(data["dirs"]["work"],
data["info"]["rgnames"]["sample"] + ".bam")
sort_bam = merge_bam_files(data["bam_files"], data["dirs"]["work"],
config, out_file=out_file)
return [[{"name": data["name"], "metadata": data["info"].get("metadata", {}),
"info": data["info"],
"genome_build": genome_build, "sam_ref": sam_ref,
"work_bam": sort_bam, "fastq1": fastq1, "fastq2": fastq2,
"dirs": data["dirs"], "config": config,
"config_file": data["config_file"]}]]