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
nextstrain · Jul 16, 2024 · 736b114 · 736b114
1 parent 87971a8
commit 736b114
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Showing 6 changed files with 4 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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
@@ -9,6 +9,7 @@ builds:
   h5n1-cattle-outbreak: ''
 
 segments:
+  - genome
   - pb2
   - pb1
   - pa

diff --git a/example_data/metadata.tsv → example_data/gisaid/metadata.tsv b/example_data/metadata.tsv → example_data/gisaid/metadata.tsv
diff --git a/example_data/ha/sequences.fasta → example_data/gisaid/sequences_ha.fasta b/example_data/ha/sequences.fasta → example_data/gisaid/sequences_ha.fasta
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,6 +9,7 @@ builds: @@
       h5n1-cattle-outbreak: ''
     segments:
+      - genome
       - pb2
       - pb1
       - pa
@@ Expand Down @@