Fix PR #87 review issues: Python bug fixes and .nf module safety

[johnoooh]

Summary

• compute_fitness.py: Add zero-guards for empty score_list (sets R=0.0) and zero Kd/KdWT values (prevents ZeroDivisionError / log(0))
• align_neoantigens_to_IEDB.py: Migrate to Bio.Align.PairwiseAligner API with fallback to deprecated pairwise2, add empty alignment guard (score=0.0), uppercase normalization on inputs
• generate_input.py: Initialize PTC_exon = None before NMD loop to prevent UnboundLocalError; guard best_pepmatch2 against None before indexing; fix typo "nonsense_nutation" → "nonsense_mutation"
• generateMutFasta.py: Fix same "nonsense_nutation" typo; add missing out_WT_fa.close() to prevent file handle leak
• netmhcpan4/main.nf and netmhcstabpan/main.nf: Replace destructive cat >> ${inputFasta} with safe cat > combined_input.fa to avoid corrupting the staged input FASTA

---

• This comment contains a description of changes (with reason).
• Check to see if a nf-core module, or subworkflow is available and usable for your pipeline.
• Feature branch is named feature/<module_name> for modules, or feature/<subworkflow_name> for subworkflows. For modules, if there is a subcommand use: feature/<module_name>/<module_subcommand>.
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs.
• Use nf-core data if possible for nf-tests. If not, use or add test data to mskcc-omics-workflows/test-datasets, following the repository guidelines, for nf-tests. Finally, if neither option is feasible, only add a stub nf-test.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label.
• Use Jfrog if possible to fulfill software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile docker
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularity
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda