Change path key in fcf outputs dict

[nevoodoo]

The outputs dict in the analysis object used a basename key to identify the file path. This is confusing as the resulting outputs file object contains both path AND basename properties. basename normally only contains the file name and extension, so use of this to denote a file path was a poor choice from myself :/

See the thread here: https://centrepopgen.slack.com/archives/C030X7WGFCL/p1743555245218149

[codecov]

Codecov Report

Attention: Patch coverage is 30.00000% with 7 lines in your changes missing coverage. Please review.

Project coverage is 82.35%. Comparing base (e2960d8) to head (c85bbd7).

Files with missing lines	Patch %	Lines
db/python/tables/output_file.py	30.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1038      +/-   ##
==========================================
- Coverage   82.56%   82.35%   -0.21%     
==========================================
  Files         189      189              
  Lines       16459    16459              
==========================================
- Hits        13589    13555      -34     
- Misses       2870     2904      +34     

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[Copilot]

Pull Request Overview

The purpose of this PR is to update the outputs dictionary to use the key "path" instead of "basename" for clarity.

• Updated test cases in test_analysis_output_files.py to use the "path" key.
• Modified production code in output_file.py to consistently refer to file paths using "path".
• Adjusted inline comments to reflect the changes.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
test/test_analysis_output_files.py	Updated test assertions to check for "path" instead of "basename".
db/python/tables/output_file.py	Modified functions and comments to use "path" consistently in file outputs.

[dancoates]

This looks like a reasonable change, as long as the stuff testing the tests is pulled out into a separate PR once you're done testing it.

The main thing that needs consideration is the backwards incompatibility of this change. I found one place that basename is being used in our code: https://github.com/populationgenomics/cpg-methods-private/blob/1954e369d9248a9557cf44084a5956d0e2986603/scripts/bioheart/update_DRAGEN_analyses.py#L73 might be good for you to have a look through too to see if I missed any

[dancoates]

Also noting there's a wip implementation here:
https://github.com/populationgenomics/production-pipelines/pull/1261/files
that would need to consider this change.