diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 16 |
1 files changed, 14 insertions, 2 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index f602681..438d4da 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -98,6 +98,14 @@ def extract_bundle(bundle: Path, workdir: Path) -> tuple[Path, tuple[Path, ...]] extractiondir = workdir.joinpath( f"{sha256_digest_over_file(bundle)}_phenotype_qc_{bundle.name}") return extractiondir, rqtl2.extract(zfile, extractiondir) +def run_qc(# pylint: disable=[too-many-arguments] + dbconn: mdb.Connection, + phenobundle: Path, + workingdir: Path, + speciesid: int, + populationid: int, + logger: Logger +) -> int: """Run quality control checks on the bundle.""" results = check_for_averages_files( **check_for_mandatory_pheno_keys( @@ -141,8 +149,12 @@ if __name__ == "__main__": main = build_main( cli_args(), - lambda dbconn, args: run_qc(dbconn, args.rqtl2bundle, _logger), + lambda dbconn, args: run_qc(dbconn, + args.rqtl2bundle, + args.working_dir, + args.speciesid, + args.populationid, + _logger), _logger, "DEBUG") sys.exit(main()) - |