Optimize qualimap performance with multi-threaded name sorting #1621
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Pre-sort BAM files by read name using samtools with multi-threading before running qualimap rnaseq. This reduces qualimap execution time by >50% (from ~85 min to <40 min) by offloading the single-threaded sorting to the multi-threaded samtools sort with the -n flag, then passing the sorted BAM to qualimap with the --sorted flag. Resolves #1356 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Add changelog entry for PR #1621 which optimizes qualimap performance through multi-threaded name sorting. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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Prevent the name-sorted BAM files created for qualimap from being published as they are only intermediate files used for performance optimization. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Add SAMTOOLS_SORT_QUALIMAP version entry to all test snapshots that run qualimap, reflecting the new samtools sort step added for performance optimization. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Increment version counts by 5 in test blocks that run qualimap to account for the additional SAMTOOLS_SORT_QUALIMAP process. Only test blocks containing QUALIMAP_RNASEQ are updated. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
MatthiasZepper
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Nov 19, 2025
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MatthiasZepper
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LGTM.
There is already a namesorting step in the UMI deduplication subworkflow, so one could possibly use the namesorted output after UMI deduplication directly for Qualimap when available and save some compute on the sorting, but this will introduce significant additional complexity.
In the interest of maintainability and modularity, I suggest to keep it this way.
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Summary
This PR optimizes the qualimap rnaseq step by pre-sorting BAM files using multi-threaded samtools before running qualimap with the
--sortedflag.Changes
SAMTOOLS_SORT_QUALIMAPprocess beforeQUALIMAP_RNASEQin the workflow-nflag for name-based sorting with multi-threading--sortedflag with pre-sorted BAM filesPerformance Impact
Based on the original issue report, this optimization reduces total execution time from ~85 minutes to under 40 minutes:
This represents a >50% reduction in execution time for the qualimap step.
Testing
Resolves #1356
🤖 Generated with Claude Code