'make_fastqs': make conda envs 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/make_fastqs_cmd.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     make_fastqs_cmd.py: implement auto process make_fastqs command
-#     Copyright (C) University of Manchester 2018-2025 Peter Briggs
+#     Copyright (C) University of Manchester 2018-2026 Peter Briggs
 #
 #########################################################################
 
@@ -392,7 +392,12 @@ def make_fastqs(ap,protocol='standard',platform=None,
     if enable_conda is None:
         enable_conda = ap.settings.conda.enable_conda
     if conda_env_dir is None:
-        conda_env_dir = ap.settings.conda.env_dir
+        if ap.settings.conda.env_dir is not 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")
 
     # Other pipeline settings
     poll_interval = ap.settings.general.poll_interval