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tgen / tempe

A container focused and streamlined iteration of the Phoenix pipeline
GNU General Public License v3.0
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Excessive CPU usage #40

Closed PedalheadPHX closed 1 year ago

PedalheadPHX commented 1 year ago

https://github.com/tgen/tempe/blob/7575cec83822ed77b0d0747e0ff3cf91dfd7a956/modules/dna_alignment/bwa_mem2_samtools.j2#L168

markdup is largely single threaded, using 20 only has an advantage for bam compression at the end, suggest 4 threads?

PedalheadPHX commented 1 year ago

This is only 4 in phoenix

bryce-turner commented 1 year ago

Fixed in https://github.com/tgen/tempe/releases/tag/v1.2.0