From 4a12b55da7b355bffd906ccef7e3368da74b2968 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Fri, 21 Jun 2024 14:12:38 -0700
Subject: [PATCH] Copy phylogenetic-ncbi to phylogenetic-fauna

Will make edits in subsequent commit to reflect the default fauna build
---
 .github/workflows/phylogenetic-fauna.yaml | 57 +++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 .github/workflows/phylogenetic-fauna.yaml

diff --git a/.github/workflows/phylogenetic-fauna.yaml b/.github/workflows/phylogenetic-fauna.yaml
new file mode 100644
index 0000000..45e286b
--- /dev/null
+++ b/.github/workflows/phylogenetic-fauna.yaml
@@ -0,0 +1,57 @@
+name: Phylogenetic NCBI
+
+defaults:
+  run:
+    # This is the same as GitHub Action's `bash` keyword as of 20 June 2023:
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell
+    #
+    # Completely spelling it out here so that GitHub can't change it out from under us
+    # and we don't have to refer to the docs to know the expected behavior.
+    shell: bash --noprofile --norc -eo pipefail {0}
+
+on:
+  workflow_dispatch:
+    inputs:
+      image:
+        description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")'
+        required: false
+        type: string
+      trial-name:
+        description: |
+          Trial name for deploying builds.
+          If not set, builds will overwrite existing builds at s3://nextstrain-data/avian-flu*
+          If set, builds will be deployed to s3://nextstrain-staging/avian-flu_trials_<trial_name>_*
+        required: false
+        type: string
+
+jobs:
+  phylogenetic:
+    permissions:
+      id-token: write
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    secrets: inherit
+    with:
+      runtime: docker
+      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 \
+          . \
+            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