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fix: Add --cores to gh actions nextstrain build
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This is required for the action to be compatible with snakemake version >5.11.0
which started to require the `--cores` option

For more context see:
- nextstrain/cli#272 
- https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1681324279363569?thread_ts=1681293140.124269&cid=C01LCTT7JNN
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corneliusroemer authored Apr 12, 2023
1 parent aa2320d commit 9b9c0f1
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1 change: 1 addition & 0 deletions .github/workflows/fetch-and-ingest.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ jobs:
ingest \
envdir env.d snakemake \
--configfiles config/config.yaml config/optional.yaml \
--cores 8 \
--printshellcmds
env:
AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
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1 change: 1 addition & 0 deletions .github/workflows/rebuild.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ jobs:
. \
envdir env.d snakemake notify_on_deploy \
--configfiles config/configfile.yaml config/nextstrain_automation.yaml \
--cores 16 \
--printshellcmds
env:
AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
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