'run_qc': create conda environments under analysis directory by default.

If the location for conda environments is not explicitly supplied or set in the configuration then default is now to create within the analysis directory.

Author: pjbriggs

auto_process_ngs/commands/run_qc_cmd.py

@@ -243,7 +243,11 @@ def run_qc(ap,projects=None,protocols=None,
     if enable_conda is None:
         enable_conda = ap.settings.conda.enable_conda
     if conda_env_dir is None:
+        # Use value from configuration
         conda_env_dir = ap.settings.conda.env_dir
+    else:
+        # Use subdirectory of analysis dir
+        conda_env_dir = os.path.join(ap.analysis_dir, "__conda", "envs")
     # Set scheduler parameters
     if poll_interval is None:
         poll_interval = ap.settings.general.poll_interval