Opt/cellbender h5 into scanpy cmd

[louisegrimble]

Description

-Updated scanpy command to read in any h5 file
-Added validation for h5 file
-Added new input_utils definition proces_h5_file()
-made appropriate changes to merge_h5ad to read in the same metadata file

Fixes #198

Some examples of the validation working as expected:

$ ./solosis-cli scrna scanpy --metadata ../../scanpy_cb.csv
  SOLOSIS    ~  version 0.4.2
INFO: Initialized with execution_uid: 92e8ae32-6c34-46a1-af35-64104b8f4e79
WARNING: Metadata file ../../scanpy_cb.csv is missing required columns: h5_path
ERROR: No valid samples provided. Use --metadata
Aborted!
lg28@farm22-head2:~/repos/solosis$ nano ../../scanpy_cb.csv 
lg28@farm22-head2:~/repos/solosis$ ./solosis-cli scrna scanpy --metadata ../../scanpy_cb.csv
  SOLOSIS    ~  version 0.4.2
INFO: Initialized with execution_uid: 9229ccfe-1629-4763-8480-3757917ab09e
WARNING: Invalid h5_path (must end with .h5): /lustre/scratch124/cellgen/haniffa/data/samples/HCA_SkO14189565/cellbender/HCA_SkO14189565_lg28_20251003_filtered
ERROR: No valid samples provided. Use --metadata
Aborted!

Type of change

• Documentation (non-breaking change that adds or improves the documentation)
• New feature (non-breaking change which adds functionality)
• Optimization (non-breaking, back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)
• Breaking change (whatever its nature)

Checklist

• All tests pass (eg. pytest)
• Pre-commit hooks run successfully (eg. pre-commit run --all-files)

[codecov]

Codecov Report

❌ Patch coverage is 35.65891% with 166 lines in your changes missing coverage. Please review.
✅ Project coverage is 62.80%. Comparing base (0ee1898) to head (5f4b5c4).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
solosis/commands/scrna/merge_h5ad.py	29.82%	40 Missing ⚠️
solosis/commands/scrna/scanpy.py	28.57%	40 Missing ⚠️
solosis/utils/input_utils.py	25.49%	38 Missing ⚠️
solosis/commands/farm/single_job.py	40.74%	16 Missing ⚠️
solosis/commands/irods/iget_cellranger.py	15.78%	16 Missing ⚠️
solosis/commands/farm/run_notebook.py	44.00%	14 Missing ⚠️
solosis/commands/alignment/cellranger_count.py	80.00%	1 Missing ⚠️
solosis/utils/lsf_utils.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #199      +/-   ##
==========================================
- Coverage   63.42%   62.80%   -0.63%     
==========================================
  Files          28       22       -6     
  Lines        1277     1285       +8     
==========================================
- Hits          810      807       -3     
- Misses        467      478      +11     

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[louisegrimble]

@barbaratpferreira Hi Barbara, this is a PR looking into how h5 files are read into the scanpy notebook. When we initially received the command/notebook from Vijay, the notebook was specifically reading in filtered_feature_bc_matrix.h5 file. After further discussions with Vijay, it was agreed that this should be changed to handle an h5 file (i.e. from cellbender, etc.). Is this how you are constructing the new scanpy notebook also? or are you expecting the filtered_feature_bc_matrix.h5 file to be read into the notebook?

[louisegrimble]

Adding @keerthi-priya-c to this conversation

[keerthi-priya-c]

Adding @keerthi-priya-c to this conversation

Hi @louisegrimble ! I agree too it should take any h5ad file submitted by user ie - either from cellranger or cellbender or soupX . If it helps in the notebook, I was testing a h5ad file from cellranger output folder when pulled in from irods-using solosis that's why it is "filtered_feature_bc_matrix.h5" in current code. but the code can be adapted to take in an h5 file in general (i.e. from celbender, cellranger or soupX etc.). I am happy to change it to adapt this or if you are already looking into this please feel free to change/adapt the code for taking in any h5ad file.