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broadinstitute / viral-pipelines

viral-ngs: complete pipelines
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WDL code/style cleanups #523

Closed dpark01 closed 8 months ago

dpark01 commented 8 months ago

This PR was originally opened to close #519 and implement runtime hinting for "Ice Lake" to speed up file localization on GCP specifically by up to 10x. It was later observed that this speedup was already happening on some critical tasks without this hinting (most likely because we were specifying LOCAL disks and/or relatively large VM shapes), so this PR no longer adds those runtime hints.

This PR is now exclusively about some cleanups to tasks to update draft-2 syntax to 1.0 for command blocks.

dpark01 commented 8 months ago

Some observations of recent runs in Terra using master branch code (ie, not the changes in the PR) suggest that the 10x localization speedup is already happening for the kraken2 and illumina_demux tasks without asking for Ice Lake specifically. I wonder if the GCE custom-shape VMs are defaulting to Ice Lake if the CPU/RAM request is high enough to begin with.