Fix Issues with Microsetta-Processing Scripts for American Gut Project Data

[l1joseph]

While initially running the TMI scripts to capture the American Gut Project microbial data, I had encountered runtime errors while running the scripts on barnacle. I encountered these issues while using the default/suggested system variables as provided on the github page.

Lucas (@lpatel) and I identified and resolved two bugs in the following files:

1. 05c.beta.sh:
   Corrected the input parameter for the k_neighbors.py script. Originally, it was using weighted_unifrac.qza as the distance matrix input. However, there was no other mention of this file elsewhere. I've updated this to weighted_normalized_unifrac.qza to match with the expected data processing flow.

2. metadata_operations.py:
   Implemented a conditional update to address a situation where the mapping dictionary could be empty, when using the AGP studies(10317) as '$STUDIES' variable. This lead to an unnecessary update to the Biom table IDs when using the AGP data for our '$STUDIES'. This change should make sure that ID updates only occur when there's actually mapping data to apply, thus preventing unnecessary calls to the 'update_ids' functions.

Affected Files:

• scripts/05c.beta.sh
• scripts/metadata_operations.py

Testing:
The fixes were tested in the same environment where the issues were initially encountered. Post-fix, the scripts ran successfully without any runtime errors, processing the American Gut Project data as expected.

Please review these changes for inclusion in the main branch to ensure a more reliable data processing experience for future users.

[lucaspatel]

Implemented a conditional update to address a situation where the mapping dictionary could be empty, when using the AGP studies(10317) as '$STUDIES' variable. This lead to an unnecessary update to the Biom table IDs when using the AGP data for our '$STUDIES'. This change should make sure that ID updates only occur when there's actually mapping data to apply, thus preventing unnecessary calls to the 'update_ids' functions.

More specifically, when $STUDIES == 10317, the mapping object is empty and the pipeline fails. This amends that.