tidy which samples get added to the sample list

grubaughlab · Aug 30, 2023 · e005e67 · e005e67
1 parent e7ce897
commit e005e67
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/denv_pipeline/utils/error_checks.py b/denv_pipeline/utils/error_checks.py
@@ -120,7 +120,6 @@ def check_env_activated():
     if pkgutil.find_loader('snakemake') is None or pkgutil.find_loader('Bio') is None:
         sys.stderr.write(green(f"Error: installation not correct. Ensure that environment is activated and you have run 'pip install .'\n"))
         sys.exit(-1)
-
 
 def check_ct_file(config):
 

diff --git a/denv_pipeline/utils/set_up_scripts.py b/denv_pipeline/utils/set_up_scripts.py
@@ -121,10 +121,12 @@ def symlink_setup(config, cwd):
 
 def get_sample_list(config):
 
+    non_sample_dirs = ["results", "log_files", "downloads"]
+
     config["sample_list"] = []
     for sample_dir in os.listdir(config["indir"]):
         if os.path.isdir(os.path.join(config["indir"], sample_dir)):
-            if sample_dir != "results" and os.path.join(config["indir"], sample_dir) != config["tempdir"] and sample_dir != "log_files":
+            if sample_dir not in non_sample_dirs and os.path.join(config["indir"], sample_dir) != config["tempdir"]:
                 config["sample_list"].append(sample_dir)
 
     return config