From b8263d243a5ace2c26b83ebf4fee093318ead1b2 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Thu, 25 Apr 2024 09:59:26 -0700 Subject: [PATCH] Specify CI target in a Snakemake rule Previously, updates to build names prompted tedious changes in downstream CI usage, such as: - https://github.com/nextstrain/augur/commit/ef79e167fff260320dba4879ed51b2164768dc5d - https://github.com/nextstrain/docker-base/commit/ebe2e5551e2fdaf057fac4238445e34f575606cf - https://github.com/nextstrain/conda-base/commit/2cda9b003af66c7eb9f606606801a5701b8cb394 Now, such changes only require updates within this pathogen repo. Co-authored-by: Jover Lee --- .github/workflows/ci.yaml | 2 +- Snakefile | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 13941bf..e753afe 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -8,4 +8,4 @@ jobs: ci: uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master with: - build-args: auspice/avian-flu_h5n1_ha_all-time.json + build-args: test_target diff --git a/Snakefile b/Snakefile index d60bc20..dc2d7c5 100755 --- a/Snakefile +++ b/Snakefile @@ -15,6 +15,12 @@ rule all: input: auspice_json = all_targets() +rule test_target: + """ + For testing purposes such as CI workflows. + """ + input: "auspice/avian-flu_h5n1_ha_all-time.json" + rule files: params: dropped_strains = "config/dropped_strains_{subtype}.txt",