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Standardize samtools version across yara/basic/optitype/subread envs

choreMaintenance, dependencies, toolingMaintenance, dependencies, tooling

Status: Open.

#137 In ylab-hi/ScanNeo2;

· riasc opened on May 25, 2026

·  

ScanNeo v0.4.x

Audit pre-execution failure modes and add graceful exits where it pays off

enhancementNew feature or requestNew feature or request

Status: Open.

#135 In ylab-hi/ScanNeo2;

· riasc opened on May 25, 2026

·  

ScanNeo v0.4.x

Convert single-command samtools shell rules to v4.0.0/bio/samtools/* wrappers (deferred low-priority)

choreMaintenance, dependencies, toolingMaintenance, dependencies, tooling

Status: Open.

#133 In ylab-hi/ScanNeo2;

· riasc opened on May 25, 2026

Prioritization rule's thread count is pinned to config["threads"] — caps binding-affinity parallelism, wastes cores on large allocations

enhancementNew feature or requestNew feature or request

Status: Open.

#120 In ylab-hi/ScanNeo2;

· riasc opened on May 22, 2026

Allow direct protein-sequence input (wildtype/mutant pairs), bypassing VCF and variant calling

enhancementNew feature or requestNew feature or request

Status: Open.

#117 In ylab-hi/ScanNeo2;

· riasc opened on May 22, 2026

·  

ScanNeo v0.4.x

Extend NMD detection and escape-rule determination to all variant sources (currently fusion-only)

enhancementNew feature or requestNew feature or request

Status: Open.

#116 In ylab-hi/ScanNeo2;

· riasc opened on May 22, 2026

·  

ScanNeo v0.4.x

Modernize the remaining Snakemake wrappers (tool-version-changing bumps)

choreMaintenance, dependencies, toolingMaintenance, dependencies, tooling

Status: Open.

#104 In ylab-hi/ScanNeo2;

· riasc opened on May 20, 2026

Bug: multi-allelic VCF entries process only last ALT's CSQ fields in variants.py

Status: Open.

#97 In ylab-hi/ScanNeo2;

· coderabbitai opened on May 20, 2026

Bug: dp computed by string concatenation instead of numeric addition in fusions.py

Status: Open.

#96 In ylab-hi/ScanNeo2;

· coderabbitai opened on May 20, 2026

Annotate neoepitopes with cancer cell fraction (CCF) / clonality

enhancementNew feature or requestNew feature or request

Status: Open.

#95 In ylab-hi/ScanNeo2;

· riasc opened on May 20, 2026

Post-run status report: per-sample rule/error triage from results and logs

enhancementNew feature or requestNew feature or request

Status: Open.

#94 In ylab-hi/ScanNeo2;

· riasc opened on May 19, 2026

Multi-sample support: process multiple samples in one run via a sample sheet

enhancementNew feature or requestNew feature or request

Status: Open.

#93 In ylab-hi/ScanNeo2;

· riasc opened on May 19, 2026