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@clingen-sthlm clingen-sthlm released this 15 Jul 14:17
· 28 commits to master since this release
v87.8.1
93e6b20

Refine FASTQ compression to Spring (#5185)

Description

This PR implements several changes to optimise FASTQ compression to Spring. The most prominent of these is a rework of the memory and time allocation to Slurm. This PR implements linear scaling of these based on the reads contained in the file (fetched from statusDB). Additionally this PR removes the --check-integrity flag passed to crunchy, since a failed compression would never pass silently.

Changed

  • Spring now uses local disk on the compute nodes as a tmp dir
  • Spring jobs are now submitted to its own partition
  • Cores/threads used reduced from 12 to 8
  • Memory and time is now set based on reads in file with fallbacks if the file does not follow the current naming pattern
  • Memory and time is significantly reduced
  • No longer passes the --check-integrity flag to crunchy
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