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theiagen / public_health_bacterial_genomics

GNU Affero General Public License v3.0
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update default mlst docker image to staphb/mlst:2.23.0 & fix CI env #163

Closed kapsakcj closed 1 year ago

kapsakcj commented 1 year ago

also removed uneccessary question mark in cpu input for mlst task

Also had to adjust the CI dependency install because importlib-metadata 5.0.0 introduced breaking changes. It now installs importlib-metadata<=4.13.0

Found this in the log.err file upon the first CI check: AttributeError: 'EntryPoints' object has no attribute 'get'

Tested with a few E. coli/Shigella in Terra here, everything ran as expected: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/22509245-3a52-48b4-9048-9d8ef915777e

kapsakcj commented 1 year ago

Just need one review here on this small change to the code - tagged a few people to see who has the bandwidth to test this dev branch out.