Pass new arguments to QC function.

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())
-