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CI: Switch CI to pathogen-repo-ci workflow #70

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Jul 16, 2024
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30 changes: 7 additions & 23 deletions .github/workflows/ci.yaml
Original file line number Diff line number Diff line change
@@ -1,28 +1,12 @@
name: CI

on:
- push
- pull_request
push:
branches:
- main
pull_request:
workflow_dispatch:

jobs:
pathogen-ci:
strategy:
matrix:
runtime: [docker, conda]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
runtime: ${{ matrix.runtime }}
run: |
nextstrain build \
phylogenetic \
--configfile build-configs/ci/config.yaml
artifact-name: output-${{ matrix.runtime }}
artifact-paths: |
phylogenetic/auspice/
phylogenetic/results/
phylogenetic/benchmarks/
phylogenetic/logs/
phylogenetic/.snakemake/log/
ci:
uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
6 changes: 6 additions & 0 deletions ingest/build-configs/ci/config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# TODO: If the ingest workflow ever runs too long, we should figure out a way
# to subset the ingest data. Currently, the CI just runs the default ingest workflow.

# Snakemake requires at least one top level key in a config file, so including
# a bogus key here that should not be used anywhere in the Snakemake workflow
bogus_ci_config: "bogus_ci_config"