diff options
Diffstat (limited to 'scripts/rqtl2')
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 7 |
1 files changed, 3 insertions, 4 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 9d58137..f602681 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -2,7 +2,6 @@ import sys import tempfile from pathlib import Path -from argparse import ArgumentParser from zipfile import ZipFile from logging import Logger, getLogger, StreamHandler @@ -12,10 +11,10 @@ from r_qtl import r_qtl2 as rqtl2 from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe -from scripts.cli_parser import init_cli_parser from uploader.files import sha256_digest_over_file from scripts.rqtl2.entry import build_main from scripts.rqtl2.cli_parser import add_bundle_argument +from scripts.cli_parser import init_cli_parser, add_global_data_arguments def validate(phenobundle: Path, logger: Logger) -> dict: """Check that the bundle is generally valid""" @@ -125,10 +124,10 @@ if __name__ == "__main__": def cli_args(): """Process command-line arguments for `install_phenos`""" - parser = add_bundle_argument(init_cli_parser( + parser = add_bundle_argument(add_global_data_arguments(init_cli_parser( program="PhenotypesQC", description=( - "Perform Quality Control checks on a phenotypes bundle file"))) + "Perform Quality Control checks on a phenotypes bundle file")))) parser.add_argument( "--working-dir", default=f"{tempfile.gettempdir()}/phenotypes_qc", |