From bb88186897b64aea58b5ccd79dcc72a4652bc454 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Mon, 21 Aug 2023 14:09:56 -0700
Subject: [PATCH] wip! workflow_dispatch

---
 .github/workflows/pathogen-repo-build.yaml    | 92 +++++++++++++++++++
 .github/workflows/pathogen-repo-build.yaml.in | 12 ++-
 2 files changed, 103 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pathogen-repo-build.yaml b/.github/workflows/pathogen-repo-build.yaml
index 94058c5..bc631c8 100644
--- a/.github/workflows/pathogen-repo-build.yaml
+++ b/.github/workflows/pathogen-repo-build.yaml
@@ -106,6 +106,98 @@ on:
           This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
         type: string
         required: false
+  workflow_dispatch:
+    inputs:
+      runtime:
+        description: >-
+          Nextstrain runtime under which to run the build. Currently only supports docker, conda, and aws-batch. Defaults to "docker".
+
+          The aws-batch runtime requires AWS credentials.  These may indirectly come from assuming a role via GitHub Actions' OIDC provider or directly from secrets.
+
+          The AWS_ROLE_ARN environment variable or GitHub Actions configuration variable is used if present.
+
+          The following secrets are used if present and no role is to be assumed:
+
+          - AWS_ACCESS_KEY_ID - AWS_SECRET_ACCESS_KEY
+
+          They must be defined in the repo's Actions secrets and passed to this workflow with `secrets: inherit`.
+        type: string
+        default: docker
+        required: false
+      run:
+        description: >-
+          The full `nextstrain build` command to run for the build. Defaults to `nextstrain build .`
+
+          Use the runtime input to select the runtime for the build instead of the runtime selection options to ensure that the runtime is properly set up within the GitHub Action job.
+
+          The pathogen repo is cloned to the top level of the working directory of the GitHub Action, so use `.` to point to the pathogen repo directory.
+
+          If your build runs longer than the 6 hour limit for GitHub Action jobs, consider using the `--detach` flag for the aws-batch runtime.
+
+          All environment variables provided via the env input and all secrets provided via `secrets: inherit` can be passed to the build runtime via the `--env` option.
+        type: string
+        default: nextstrain build .
+        required: false
+      env:
+        description: >-
+          Environment variables to set for this reusable workflow since environment variables in the caller workflow are not propagated to reusable workflows. This is expected to be a string containing YAML.
+
+          This is easily produced, for example, by pretending you're writing normal nested YAML within a literal multi-line block scalar (introduced by "|"):
+
+
+            with:
+              env: |
+                FOO: bar
+                I_CANT_BELIEVE: "it's not YAML"
+                would_you_believe: |
+                  it's
+                  not
+                  yaml
+
+          Do not use for secrets!  Instead, pass them via GitHub Action's dedicated secrets mechanism.
+        type: string
+        default: ""
+        required: false
+      artifact-name:
+        description: >-
+          Name to use for the build output artifact uploaded at end of the workflow.
+
+          If you're invoking this workflow multiple times from the same calling workflow, you should set this. Otherwise, the default "build-outputs" is probably fine.
+        type: string
+        default: build-outputs
+        required: false
+      artifact-paths:
+        description: >-
+          List of paths to include in the build output artifact uploaded at the end of the workflow, as a string following the format of the `paths` input of the `actions/upload-artifact` action. For example:
+
+
+            with:
+              artifact-paths: |
+                results/
+                auspice/
+                logs/
+
+          The default paths included in the artifact are:
+
+
+            build.log
+            auspice/
+            results/
+            benchmarks/
+            logs/
+            .snakemake/log/
+
+          The "build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
+
+          This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
+        type: string
+        required: false
+      repo:
+        description: >-
+          Repository name with owner (e.g. nextstrain/zika).
+        type: string
+        default: ""
+        required: true
 env:
   NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
 permissions:
diff --git a/.github/workflows/pathogen-repo-build.yaml.in b/.github/workflows/pathogen-repo-build.yaml.in
index 06ad60e..5cb9f10 100644
--- a/.github/workflows/pathogen-repo-build.yaml.in
+++ b/.github/workflows/pathogen-repo-build.yaml.in
@@ -14,7 +14,7 @@ defaults:
 
 on:
   workflow_call:
-    inputs:
+    inputs: &inputs
       repo:
         description: >-
           Repository name with owner (e.g. nextstrain/zika). Defaults to the
@@ -140,6 +140,16 @@ on:
         type: string
         required: false
 
+  workflow_dispatch:
+    inputs:
+      <<: *inputs
+      repo:
+        description: >-
+          Repository name with owner (e.g. nextstrain/zika).
+        type: string
+        default: ""
+        required: true
+
 env:
   NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github