fix: improve error handling for subprocess commands in atac_seq.py

[Bento007]

Reason for Change

Notes for Reviewer

[Copilot]

Pull Request Overview

This PR improves error handling for subprocess commands in the ATAC-seq pipeline by adding comprehensive error checking for all processes in the command pipelines. Previously, only the final bgzip process was checked for errors, potentially allowing earlier pipeline failures to go unnoticed.

• Enhanced error handling to check return codes of all subprocess commands in pipelines
• Consolidated error reporting by collecting all failures and presenting them together
• Replaced single-process error checking with comprehensive multi-process validation

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[codecov]

Codecov Report

❌ Patch coverage is 57.14286% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.50%. Comparing base (473500e) to head (6133b95).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1446      +/-   ##
==========================================
- Coverage   88.69%   88.50%   -0.20%     
==========================================
  Files          23       23              
  Lines        2646     2662      +16     
==========================================
+ Hits         2347     2356       +9     
- Misses        299      306       +7     

Components	Coverage Δ
cellxgene_schema_cli	88.82% <57.14%> (-0.26%)	⬇️
migration_assistant	91.26% <ø> (ø)
schema_bump_dry_run_genes	79.74% <ø> (ø)
schema_bump_dry_run_ontologies	99.51% <ø> (ø)

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