Set BWA and bwamem2 index memory dynamically #6628
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This one doesn't fail, but it's good practice.
edmundmiller
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I like it 👍 it’ll also play nice with the new resourceLimits directive |
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I was talking to @drpatelh about this earlier this week. Sounds good. Very neat if it scales in such a linear way. Should we add a baseline of additional memory? |
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Closes nf-core/sarek#1377 |
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What can we do for bwa mem and bwamem2 mem? |
What do you mean? |
matthdsm
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Oct 15, 2024
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Kept having bwamem2 index tasks that ran forever and failed.
Updated bwamem2 to use 28.B of memory per byte of fasta. Issue for reference: bwa-mem2/bwa-mem2#9
Also tracked down the required memory for bwa index while I was at it. Doesn't seem to fail because most of the genome requirements are under the necessary memory.
Not the first place where people have run into this #6628