Update version, dependencies, and improve file checks

[willisbillis]

Reflect updates in the version and release date in CITATION.cff. Enhance the environment configuration for Ubuntu. Improve data processing scripts by adding file existence checks and logging warnings for missing files. Adjust grouping variables in VlnPlot for consistency in patient ID assignments.

Summary by Sourcery

Update environment dependencies, add file existence checks with warnings in aggregation scripts, standardize grouping variables in R pipeline, and refresh citation metadata.

Enhancements:

• Upgrade multiple package versions in the Ubuntu environment configuration
• Add file existence checks and log warnings for missing files in RNA and ATAC aggregation scripts
• Use HTO_maxID and HTO_classification for VlnPlot grouping and patient_id assignments in the R QC pipeline

Documentation:

• Update CITATION.cff to reflect the new version and release date

[sourcery-ai]

Reviewer's Guide

This PR updates environment dependency versions in the Ubuntu configuration, adds file existence checks with warnings in the cellranger aggregation scripts, refines grouping variables and patient ID assignments in QC R scripts to use HTO-based identifiers, and bumps the version and release date in the CITATION metadata.

Class diagram for updated grouping and patient ID assignment in QC R scripts

classDiagram
    class sc_total {
        library_id : string
        patient_id : string
        HTO_maxID : string
        HTO_classification : string
        # MULTI_ID : string (replaced)
        # MULTI_classification : string (replaced)
        sample_id : string
    }

    class VlnPlot {
        +plot(features, group.by, ...)
    }

    sc_total "1" -- "*" VlnPlot : used in

    %% Notes on changes:
    %% - group.by in VlnPlot now uses HTO_maxID and HTO_classification instead of MULTI_ID and MULTI_classification
    %% - patient_id assignment now uses HTO_maxID instead of MULTI_ID
    %% - MULTI_ID and MULTI_classification are replaced by HTO-based fields

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Flow diagram for file existence checks in aggregation scripts

flowchart TD
    A[Start aggregation script] --> B{For each sample}
    B --> C[Determine file paths]
    C --> D{Do all required files exist?}
    D -- Yes --> E[Append sample info to AGGR_CSV]
    D -- No --> F[Log warning and skip sample]
    E --> G[Next sample]
    F --> G
    G --> B
    B --> H[End]

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File-Level Changes

Change	Details	Files
Update Ubuntu environment package versions	Bumped system library revisions (e.g. binutils_impl, ld_impl, libsqlite, libwebp-base) Upgraded Python and R packages (e.g. ca-certificates, certifi, pandas, narwhals, r/commonmark, r/cowplot, statsmodels, uv)	environment_ubuntu-latest.yml
Add file existence checks with warning logs in aggregation scripts	Wrap existing record writes in file-present conditionals Emit warnings and skip entries when RNA/ATAC files are missing	src/aggr_template/pipeline/RNA.FB.VDJ/run_cellranger.aggr_rna.sh src/aggr_template/pipeline/ATAC.ASAP/run_cellranger.aggr_atac.sh
Refine QC scripts to use HTO identifiers for grouping and patient IDs	Replace MULTI_ID/classification with HTO_maxID/classification in VlnPlot calls Adjust patient_id assignment and filtering to reference HTO_maxID	src/phase2_scripts/LRA/run_phase2.QC_LRA_rna.R
Bump version and release date in CITATION metadata	Updated version number Updated release date	CITATION.cff

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