phylo fixes #13
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phylo fixes #13
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Make sure the phylo GH Action workflow is properly triggered after a successful run of the 'Fetch and ingest' workflow.
Previously used `--nthread auto` which would let each tree/align command use _all_ available cores. Since this is not done with Snakemake threads, Snakemake is not aware of this usage and will end up scheduling of multiple jobs that would oversubscribe. This results in out of memory errors when running the workflow locally and likely also the reason for the failed GH Action workflow.¹ This commit adds a hardcoded Snakemake thread so that Snakemake can properly schedule the jobs based on available cores. If the single threaded jobs take too long, then we can bump the threads and/or transition to running phylo on AWS Batch. ¹ <https://github.com/nextstrain/chikv/actions/runs/20007579231>
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Phylo workflow successfully completed in 1hr4m which seems reasonable to me considering there are 6 different builds. Builds are available on staging. |
Contributor
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Merging this ahead of tomorrow's automated workflow. We can optimize runtime/threads later. |
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Description of proposed changes
A couple fixes since I noticed the phylo workflow failed and has not been automatically triggered by the weekly ingest workflow on the status page
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