in app/source/dragen/src/dragen_qs.py [0:0]
def __init__(self, dragen_args):
self.orig_args = dragen_args
self.new_args = copy.copy(dragen_args)
# Inputs needed for downloading
self.ref_dir = None # Create local directory to download reference
self.input_dir = None # Create local directory for Dragen input info
self.ref_s3_url = None # Determine from the -r or --ref-dir option
self.ref_s3_index = -1
self.fastq_list_url = None # Determine from the --fastq-list option
self.fastq_list_index = -1
self.tumor_fastq_list_url = None # Determine from the --tumor-fastq-list option
self.tumor_fastq_list_index = -1
self.vc_tgt_bed_url = None # Determine from the --vc-target-bed option
self.vc_tgt_bed_index = -1
self.vc_depth_url = None # Determine from the ----vc-depth-intervals-bed
self.vc_depth_index = -1
self.cnv_normals_list_url = None # Determine from --cnv-normals-list option
self.cnv_normals_index = -1
self.cnv_target_bed_url = None # Determine from --cnv-target-bed option
self.cnv_target_index = -1
self.dbsnp_url = None # Determine from --dbsnp option
self.dbsnp_index = -1
self.cosmic_url = None # Determine from --cosmic option
self.cosmic_index = -1
self.qc_cross_cont_vcf_url = None # Determine from --qc-cross-cont-vcf-url
self.qc_cross_cont_vcf_index = -1
self.qc_coverage_region_1_url = None # Determine from --qc-coverage-region-1
self.qc_coverage_region_1_index = -1
self.qc_coverage_region_2_url = None # Determine from --qc-coverage-region-2
self.qc_coverage_region_2_index = -1
self.qc_coverage_region_3_url = None # Determine from --qc-coverage-region-3
self.qc_coverage_region_3_index = -1
# Output info
self.output_s3_url = None # Determine from the --output-directory field
self.output_s3_index = -1
self.output_dir = None # Create local output directory for current dragen process
# Run-time variables
self.input_dir = None # Create local output directory for current dragen process
self.process_start_time = None # Process start time
self.process_end_time = None # Process end time
self.global_exit_code = 0 # Global exit code. If any process fails then we exit with a non-zero status
self.set_resource_limits()
self.parse_download_args()