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Update BWA_INDEX memory formula to match BWAMEM2_INDEX pattern
PR checklist
- [x] This comment contains a description of changes (with reason).
- [x] If you've fixed a bug or added code that should be tested, add tests!
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Description
BWA_INDEX fails on HPC systems with strict memory limits. Applied the same memory allocation pattern used in BWAMEM2_INDEX.
Changes
Updated modules/nf-core/bwa/index/main.nf:
- memory { 6.B * fasta.size() }
+ memory { (53.7.MB * Math.ceil(fasta.size() / 10000000)) * task.attempt }
- Floor-based allocation: 53.7MB minimum (5.37x per BWA docs)
task.attemptmultiplier enables retry with increased memory on failure- Maintains 5.37x scaling:
53.7MB / 10MB = 5.37
Identical pattern to BWAMEM2_INDEX (28x scaling, 280MB floor).
Original prompt
This section details on the original issue you should resolve
<issue_title>BWA_INDEX just needs an update like BWAMEM2_INDEX in PR#8993</issue_title> <issue_description>It's failing on some HPC systems</issue_description>
<agent_instructions>Update the memory request for BWA_INDEX just like the memory request in BWAMEM2_index but with the values specific for BWA_INDEX</agent_instructions>
Comments on the Issue (you are @copilot in this section)
- Fixes nf-core/modules#9527
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