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"]}]]