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phylogenetic-fauna: Update for default builds with fauna data
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I think the diff in this commit warrants maintaining separate
GH Action workflows for NCBI vs fauna data builds instead of trying to
shoehorn both into a single complicated GH Action workflow.

Uses AWS Batch runtime with cpus/memory according to the repo's README
instructions.¹

¹ <https://github.com/nextstrain/avian-flu/blob/4ae5e32af0f00b3120d040bfd0b527a4b2c51c09/README.md?plain=1#L14>
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joverlee521 committed Jun 21, 2024
1 parent 4a12b55 commit 08ae7e0
Showing 1 changed file with 7 additions and 8 deletions.
15 changes: 7 additions & 8 deletions .github/workflows/phylogenetic-fauna.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: Phylogenetic NCBI
name: Phylogenetic Fauna

defaults:
run:
Expand Down Expand Up @@ -31,27 +31,26 @@ jobs:
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
runtime: docker
runtime: aws-batch
run: |
declare -a config;
config+=(
s3_src="s3://nextstrain-data/files/workflows/avian-flu/h5n1"
);
if [[ "$TRIAL_NAME" ]]; then
config+=(
deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_"
)
fi;
nextstrain build \
--detach \
--no-download \
--cpus 16 \
--memory 28800mib \
. \
deploy_all \
--snakefile Snakefile.genome \
--config "${config[@]}"
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
TRIAL_NAME: ${{ inputs.trial-name }}
artifact-name: phylogenetic-full-genome-build-output
artifact-name: phylogenetic-fauna-build-output

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