def setup_args(parser): parser.add_argument( "template", help=( "Template name or path to template YAML file. " "Built in choices: freebayes-variant, gatk-variant, tumor-paired, " "noalign-variant, illumina-rnaseq, illumina-chipseq")) parser.add_argument( "metadata", help= "CSV file with project metadata. Name of file used as project name.") parser.add_argument("input_files", nargs="*", help="Input read files, in BAM or fastq format") parser.add_argument("--only-metadata", help="Ignore samples not present in metadata CSV file", action="store_true", default=False) parser.add_argument("--force-single", help="Treat all files as single reads", action="store_true", default=False) parser.add_argument( "--separators", help= "semicolon separated list of separators that indicates paired files.", default="R,_,-,.") setup_script_logging() return parser
def setup_args(parser): parser.add_argument("template", help=("Template name or path to template YAML file. " "Built in choices: freebayes-variant, gatk-variant, tumor-paired, " "noalign-variant, illumina-rnaseq, illumina-chipseq")) parser.add_argument("metadata", help="CSV file with project metadata. Name of file used as project name.") parser.add_argument("input_files", nargs="*", help="Input read files, in BAM or fastq format") parser.add_argument("--only-metadata", help="Ignore samples not present in metadata CSV file", action="store_true", default=False) setup_script_logging() return parser
def setup_logging(): setup_script_logging()
def setup_logging(): setup_script_logging()