Created the new scanpy workflow

[vjbaskar]

Description

Updated per sample rna-seq processing pipeline. The main change is python. notebook. Changed the scanpy.py command to accomodate the changes in the notebook.

Fixes # Issue with how one can use the same ipykernel and environment. Numpy deprecated function fixed with new scanpy env.

Type of change

• 🐛 Bug fix (non-breaking change that resolves an issue)
• ✨ New feature (non-breaking change that adds functionality)
• ⚡ Optimisation (non-breaking improvement to performance or efficiency)
• 🧩 Documentation (adds or improves documentation)
• 🧱 Maintenance (refactor, dependency update, CI/CD, etc.)
• 🔥 Breaking change (fix or feature that causes existing functionality to change)

Checklist

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

[louisegrimble]

@vm11 found that the outputs generated (WS_wEMB10202354.h5ad) do not match sample ID that I inputted (HCA_SkO13919077) into solosis. I also inputted two samples and only 1 output was generated.

-rw-rw-r--  1 lg28 team298     96041 Dec  4 10:04 low_quality_cells_removed_in_preQC_WS_wEMB10202354.json
-rw-rw-r--  1 lg28 team298 213836117 Dec  4 10:14 WS_wEMB10202354.h5ad
-rw-rw-r--  1 lg28 team298   1137998 Dec  4 10:14 HCA_SkO13919077_HCA_SkO13919077.ipynb

## and here
$ ls -lrt reports
total 56
drwxr-xr-x 3 lg28 team298  804 Dec  4 10:08 WS_wEMB10202354
-rw-r--r-- 1 lg28 team298 2199 Dec  4 10:14 index.html

index.html also didn't generate any plots

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