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()
