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sanger-tol / treeval

Pipelines for the production of Treeval data
https://pipelines.tol.sanger.ac.uk/treeval
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Update GitHub CI run on large paid Github runner #184

Closed weaglesBio closed 7 months ago

weaglesBio commented 9 months ago

Description of feature

As per Matthieu's message:

just updated genomeassembly to use larger machines on GitHub CI: https://github.com/sanger-tol/genomeassembly/pull/23/files#diff-b803fcb7f17ed9235f1e5cb1fcd2f5d3b2838429d4368ae4c57ce4436577f03fR25 Those machines are available for TreeVal too, and you could then get rid of https://github.com/sanger-tol/treeval/blob/dev/subworkflows/local/hic_mapping.nf#L173-L182 With some luck, all you need to do is to change the runs-on line highlighted above to one of these: ubuntu2204-4c 4-cores · 16 GB RAM · 150 GB SSD ubuntu2204-8c 8-cores · 32 GB RAM · 300 GB SSD ubuntu2204-16c 16-cores · 64 GB RAM · 600 GB SSD ubuntu2204-32c 32-cores · 128 GB RAM · 1200 GB SSD But that didn’t work for hifiasm under Docker. Guoying had to switch to Singularity instead (see the rest of that PR)

DLBPointon commented 7 months ago

Optimizations done so far have eliminated the need for the paid runner.

A full test has, however, been implemented and works as off #195