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Convert single-command samtools shell rules to v4.0.0/bio/samtools/* wrappers (deferred low-priority)
choreMaintenance, dependencies, toolingMaintenance, dependencies, toolingStatus: Open.#133 In ylab-hi/ScanNeo2;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 requestStatus: Open.#120 In ylab-hi/ScanNeo2;Modernize the remaining Snakemake wrappers (tool-version-changing bumps)
choreMaintenance, dependencies, toolingMaintenance, dependencies, toolingStatus: Open.#104 In ylab-hi/ScanNeo2;- Status: Open.#97 In ylab-hi/ScanNeo2;
Annotate neoepitopes with cancer cell fraction (CCF) / clonality
enhancementNew feature or requestNew feature or requestStatus: Open.#95 In ylab-hi/ScanNeo2;Multi-sample support: process multiple samples in one run via a sample sheet
enhancementNew feature or requestNew feature or requestStatus: Open.#93 In ylab-hi/ScanNeo2;Preserve short wt sequences and rework self_similarity for different-length inputs
enhancementNew feature or requestNew feature or requestStatus: Open.#89 In ylab-hi/ScanNeo2;Add resource declarations (mem_mb) to resource-intensive rules
enhancementNew feature or requestNew feature or requestStatus: Open.#66 In ylab-hi/ScanNeo2;- Status: Open.