add more friendly message when skipping refinery

rhysnewell · Jul 28, 2023 · 0ff4bc3 · 0ff4bc3
1 parent cb0b0b6
commit 0ff4bc3
Showing 1 changed file with 9 additions and 5 deletions.
diff --git a/aviary/modules/binning/scripts/run_checkm.py b/aviary/modules/binning/scripts/run_checkm.py
@@ -4,14 +4,18 @@
 from pathlib import Path
 
 def checkm(checkm2_db, bin_folder, bin_ext, refinery_max_iterations, output_folder, output_file, threads):
-    if len([f for f in os.listdir(bin_folder) if f.endswith(bin_ext)]) > 0 and refinery_max_iterations > 0:
-        print(f"Using CheckM2 database {checkm2_db}/uniref100.KO.1.dmnd")
-        subprocess.run(f"CHECKM2DB={checkm2_db}/uniref100.KO.1.dmnd checkm2 predict -i {bin_folder}/ -x {bin_ext} -o {output_folder} -t {threads} --force")
-        shutil.copy(f"{output_folder}/quality_report.tsv", output_file)
-    else:
+    if len([f for f in os.listdir(bin_folder) if f.endswith(bin_ext)]) == 0:
         print(f"No bins found in {bin_folder}")
         os.makedirs(output_folder)
         Path(output_file).touch()
+    elif refinery_max_iterations == 0:
+        print("Skipping pre-refinery CheckM2 rules")
+        os.makedirs(output_folder)
+        Path(output_file).touch()
+    else:
+        print(f"Using CheckM2 database {checkm2_db}/uniref100.KO.1.dmnd")
+        subprocess.run(f"CHECKM2DB={checkm2_db}/uniref100.KO.1.dmnd checkm2 predict -i {bin_folder}/ -x {bin_ext} -o {output_folder} -t {threads} --force")
+        shutil.copy(f"{output_folder}/quality_report.tsv", output_file)
 
 
 if __name__ == '__main__':