From 736b114f5b6c783a5a56c1c9f4cbc9a0fe9e6c65 Mon Sep 17 00:00:00 2001
From: james hadfield <hadfield.james@gmail.com>
Date: Tue, 16 Jul 2024 13:35:53 +1200
Subject: [PATCH] Update GitHub Actions invocations

to reflect the changes made in the previous few commits.

The addition of "genome" to the h5n1-cattle-outbreak config YAML is
needed to make it an explicit output of the `all` rule, and this output
is what's used by the `deploy_all` rule
---
 .github/workflows/ci.yaml                                   | 2 +-
 .github/workflows/phylogenetic-fauna.yaml                   | 1 +
 .github/workflows/phylogenetic-ncbi.yaml                    | 6 +-----
 config/h5n1-cattle-outbreak.yaml                            | 1 +
 example_data/{ => gisaid}/metadata.tsv                      | 0
 .../{ha/sequences.fasta => gisaid/sequences_ha.fasta}       | 0
 6 files changed, 4 insertions(+), 6 deletions(-)
 rename example_data/{ => gisaid}/metadata.tsv (100%)
 rename example_data/{ha/sequences.fasta => gisaid/sequences_ha.fasta} (100%)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 3d45e5a..000ec5c 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -11,4 +11,4 @@ jobs:
     # conform since this is a collaborative repo with an external group.
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0
     with:
-      build-args: test_target
+      build-args: --configfile config/gisaid.yaml -pf test_target
diff --git a/.github/workflows/phylogenetic-fauna.yaml b/.github/workflows/phylogenetic-fauna.yaml
index 482de73..2abff69 100644
--- a/.github/workflows/phylogenetic-fauna.yaml
+++ b/.github/workflows/phylogenetic-fauna.yaml
@@ -48,6 +48,7 @@ jobs:
           --memory 28800mib \
           . \
             deploy_all \
+            --configfile config/gisaid.yaml \
             --config "${config[@]}"
 
       env: |
diff --git a/.github/workflows/phylogenetic-ncbi.yaml b/.github/workflows/phylogenetic-ncbi.yaml
index 3013611..096e0f1 100644
--- a/.github/workflows/phylogenetic-ncbi.yaml
+++ b/.github/workflows/phylogenetic-ncbi.yaml
@@ -42,10 +42,6 @@ jobs:
       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}_"
@@ -55,7 +51,7 @@ jobs:
         nextstrain build \
           . \
             deploy_all \
-            --snakefile Snakefile.genome \
+            --configfile config/h5n1-cattle-outbreak.yaml \
             --config "${config[@]}"
 
       env: |
diff --git a/config/h5n1-cattle-outbreak.yaml b/config/h5n1-cattle-outbreak.yaml
index a360f93..e69dd4b 100644
--- a/config/h5n1-cattle-outbreak.yaml
+++ b/config/h5n1-cattle-outbreak.yaml
@@ -9,6 +9,7 @@ builds:
   h5n1-cattle-outbreak: ''
 
 segments:
+  - genome
   - pb2
   - pb1
   - pa
diff --git a/example_data/metadata.tsv b/example_data/gisaid/metadata.tsv
similarity index 100%
rename from example_data/metadata.tsv
rename to example_data/gisaid/metadata.tsv
diff --git a/example_data/ha/sequences.fasta b/example_data/gisaid/sequences_ha.fasta
similarity index 100%
rename from example_data/ha/sequences.fasta
rename to example_data/gisaid/sequences_ha.fasta