From 1eba5c0ccf0991f4c3a4ade1103349ff59ad051f Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 31 May 2024 11:32:44 -0700
Subject: [PATCH 01/12] Add names to all steps [#89]

---
 .github/workflows/pathogen-repo-ci.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index d4a9f9e..5e2d18b 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -196,7 +196,8 @@ jobs:
           '
           | tee -a "$GITHUB_ENV"
 
-      - uses: actions/checkout@v4
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
           repository: ${{ inputs.repo }}
 
@@ -226,7 +227,8 @@ jobs:
       #   approach. -trs ]
       #
       #   -trs, 28 April 2022
-      - uses: nextstrain/.github/actions/setup-nextstrain-cli@c1191de9d5e1a30e91d70b0fd1041d97ed1b2496
+      - name: Setup Nextstrain
+        uses: nextstrain/.github/actions/setup-nextstrain-cli@c1191de9d5e1a30e91d70b0fd1041d97ed1b2496
         with:
           runtime: ${{ matrix.runtime }}
 

From 6d8f90133ab54b562e8bac375fe5cc67d14f7b6b Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 31 May 2024 11:32:56 -0700
Subject: [PATCH 02/12] Remove example-data copy step [#89]

This should be handled within the build-config of the consuming repo
if it is required.
---
 .github/workflows/pathogen-repo-ci.yaml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 5e2d18b..a8ce20e 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -232,14 +232,6 @@ jobs:
         with:
           runtime: ${{ matrix.runtime }}
 
-      - name: Copy example data
-        run: |
-          if [[ -d example_data ]]; then
-            mkdir -p data/
-            cp -r -v example_data/* data/
-          else
-            echo No example data to copy.
-          fi
 
       - run: nextstrain build . ${{ inputs.build-args }}
 

From d3730bc790d3e3d8a9fe05ae98ef2ecfa66c8670 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 31 May 2024 11:33:29 -0700
Subject: [PATCH 03/12] Refactor `pathogen-repo-ci` to be smarter [#89]

Also update nextstrain runtime setup step to use "modern" sidecar
version, which has the side effect/benefit of allowing the
`run-nexstrain-build` action to also be invoked from the sidecar
instead of pinned to `master` or some other version.
---
 .github/workflows/pathogen-repo-ci.yaml       | 88 ++++++++++---------
 README.md                                     |  1 +
 actions/run-nextstrain-build-step/action.yaml | 39 ++++++++
 actions/setup-nextstrain-cli/action.yaml      |  4 -
 4 files changed, 88 insertions(+), 44 deletions(-)
 create mode 100644 actions/run-nextstrain-build-step/action.yaml

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index a8ce20e..b7cef89 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -3,6 +3,15 @@
 # workflow) in this repo for an example of what the caller workflow looks like.
 name: CI
 
+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_call:
     inputs:
@@ -85,8 +94,12 @@ on:
 
 permissions:
   contents: read
+  id-token: write
   packages: read
 
+env:
+  NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
+
 jobs:
   configuration:
     runs-on: ubuntu-latest
@@ -101,8 +114,17 @@ jobs:
     outputs:
       runtimes: ${{ steps.inputs.outputs.runtimes }}
 
-  build:
-    needs: configuration
+  workflow-context:
+    runs-on: ubuntu-latest
+    steps:
+      - id: workflow-context
+        uses: nextstrain/.github/actions/workflow-context@master
+    outputs:
+      repository: ${{ steps.workflow-context.outputs.repository }}
+      sha: ${{ steps.workflow-context.outputs.sha }}
+
+  nextstrain-build:
+    needs: [configuration, workflow-context]
     strategy:
       fail-fast: false
       matrix:
@@ -201,47 +223,33 @@ jobs:
         with:
           repository: ${{ inputs.repo }}
 
-      # XXX TODO: It would be better for this to call setup-nextstrain-cli
-      # using the same ref that this workflow was called with (e.g. if this
-      # workflow was invoked by the caller workflow with @foo than we invoke
-      # the action with @foo too), but it's not currently possible to figure
-      # out that ref.  See discussion around this (including results of some
-      # investigation I did):
-      #
-      #   - https://github.community/t/reusable-workflows-get-the-ref-inside-the-called-workflow/224109
-      #   - https://github.community/t/ref-head-in-reusable-workflows/203690/92
-      #
-      # Once we can figure out that ref, then we can actions/checkout our
-      # nextstrain/.github repo at that ref as a sidecar path somewhere and
-      # then invoke the setup-nextstrain-cli action using a local file path
-      # instead of a remote owner/repo path.  This separate checkout will be
-      # necessary since the "uses:" key can't be interpolated (${{…}}) with
-      # context vars.
-      #
-      # For now, update the hardcoded ref (e.g. @90af34…) below when you make
-      # future changes to setup-nextstrain-cli.
-      #
-      # [ Update 16 Feb 2024: We solved this for pathogen-repo-build.yaml, but
-      #   because it required a new permission on the GitHub tokens (id-token:
-      #   write) we decided not to update this workflow (yet?) to use the same
-      #   approach. -trs ]
-      #
-      #   -trs, 28 April 2022
-      - name: Setup Nextstrain
-        uses: nextstrain/.github/actions/setup-nextstrain-cli@c1191de9d5e1a30e91d70b0fd1041d97ed1b2496
+      - # Need to run this after the build repo is cloned so that cloning the
+        # build repo does not overwrite the .git dir and remove the extra support files
+        # that we need from nextstrain/.github repo
+        name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
+        uses: actions/checkout@v4
         with:
+          repository: ${{ needs.workflow-context.outputs.repository }}
+          ref: ${{ needs.workflow-context.outputs.sha }}
+          path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
+
+      - name: Setup Nextstrain runtime ${{ matrix.runtime }}
+        uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
+        with:
+          cli-version: ">=8.3.0"
           runtime: ${{ matrix.runtime }}
 
+      - name: Run ingest
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build-step
+        with:
+          step: ingest
 
-      - run: nextstrain build . ${{ inputs.build-args }}
+      - name: Run phylogenetic
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build-step
+        with:
+          step: phylogenetic
 
-      - if: always()
-        uses: actions/upload-artifact@v4
+      - name: Run nextclade
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build-step
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
-          path: |
-            auspice/
-            results/
-            benchmarks/
-            logs/
-            .snakemake/log/
+          step: nextclade
diff --git a/README.md b/README.md
index 261e48e..686df0e 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,7 @@ See also GitHub's [documentation on issue and PR templates](https://docs.github.
 
 Invoked by our GitHub Actions workflows, including the reusable workflows below.
 
+- [Run Nextstrain Build Step](actions/run-nextstrain-build-step/action.yaml)
 - [Setup Nextstrain CLI](actions/setup-nextstrain-cli/action.yaml)
 - [shellcheck](actions/shellcheck/action.yaml)
 - [Setup SSH](actions/setup-ssh/action.yaml) access to runner machine
diff --git a/actions/run-nextstrain-build-step/action.yaml b/actions/run-nextstrain-build-step/action.yaml
new file mode 100644
index 0000000..f3900be
--- /dev/null
+++ b/actions/run-nextstrain-build-step/action.yaml
@@ -0,0 +1,39 @@
+name: run-nextstrain-build-step
+description: >-
+  Runs a single `nextstrain build` command in a given sub-directory of
+  a pathogen repo. Must be provided with the name of the
+  sub-directory.
+
+inputs:
+  step:
+    description: The name of the sub-directory to run the build from
+    type: string
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - id: run-build
+      env:
+        STEP: ${{ inputs.step }}
+      run: |
+        if [[ -f nextstrain-pathogen.yaml && -f $STEP/Snakefile && -f $STEP/build-configs/ci/config.yaml ]]; then
+          nextstrain build $STEP --configfile build-configs/ci/config.yaml
+        else
+          echo "Skipping $STEP build due to one or more missing files."
+          for i in nextstrain-pathogen.yaml $STEP/Snakefile $STEP/build-configs/ci/config.yaml; do
+            ! test -f $i && echo missing $i
+          done
+        fi
+      shell: bash
+
+    - id: upload-artifact
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{inputs.step }}-outputs-${{ matrix.runtime }}
+        path: |
+          ${{ inputs.step }}/results/
+          ${{ inputs.step }}/benchmarks/
+          ${{ inputs.step }}/logs/
+          ${{ inputs.step }}/.snakemake/log/
diff --git a/actions/setup-nextstrain-cli/action.yaml b/actions/setup-nextstrain-cli/action.yaml
index ace540a..be6db12 100644
--- a/actions/setup-nextstrain-cli/action.yaml
+++ b/actions/setup-nextstrain-cli/action.yaml
@@ -1,7 +1,3 @@
-# If you update this action, please update the hardcoded ref to it in
-# .github/workflows/pathogen-repo-ci.yaml.  See the commentary there for why
-# it's necessary.
-
 name: Setup Nextstrain CLI
 description: >-
   This GitHub Actions action is intended to be called by workflows in our other

From f8e003c27ae5643ed1572c6d0b7246bc05dac535 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 31 May 2024 17:24:05 -0700
Subject: [PATCH 04/12] Renaming things per PR feedback [#89]

* run-nextstrain-build-step -> run-nextstrain-build
* inputs.step -> inputs.directory
---
 .github/workflows/pathogen-repo-ci.yaml       | 16 ++++----
 README.md                                     |  2 +-
 actions/run-nextstrain-build-step/action.yaml | 39 -------------------
 actions/run-nextstrain-build/action.yaml      | 39 +++++++++++++++++++
 4 files changed, 48 insertions(+), 48 deletions(-)
 delete mode 100644 actions/run-nextstrain-build-step/action.yaml
 create mode 100644 actions/run-nextstrain-build/action.yaml

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index b7cef89..458baa2 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -218,7 +218,7 @@ jobs:
           '
           | tee -a "$GITHUB_ENV"
 
-      - name: Checkout repo
+      - name: Checkout ${{ inputs.repo }}
         uses: actions/checkout@v4
         with:
           repository: ${{ inputs.repo }}
@@ -233,23 +233,23 @@ jobs:
           ref: ${{ needs.workflow-context.outputs.sha }}
           path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
 
-      - name: Setup Nextstrain runtime ${{ matrix.runtime }}
+      - name: Set up Nextstrain runtime ${{ matrix.runtime }}
         uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
         with:
           cli-version: ">=8.3.0"
           runtime: ${{ matrix.runtime }}
 
       - name: Run ingest
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build-step
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
         with:
-          step: ingest
+          directory: ingest
 
       - name: Run phylogenetic
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build-step
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
         with:
-          step: phylogenetic
+          directory: phylogenetic
 
       - name: Run nextclade
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build-step
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
         with:
-          step: nextclade
+          directory: nextclade
diff --git a/README.md b/README.md
index 686df0e..cb31d92 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ See also GitHub's [documentation on issue and PR templates](https://docs.github.
 
 Invoked by our GitHub Actions workflows, including the reusable workflows below.
 
-- [Run Nextstrain Build Step](actions/run-nextstrain-build-step/action.yaml)
+- [Run Nextstrain Build](actions/run-nextstrain-build/action.yaml)
 - [Setup Nextstrain CLI](actions/setup-nextstrain-cli/action.yaml)
 - [shellcheck](actions/shellcheck/action.yaml)
 - [Setup SSH](actions/setup-ssh/action.yaml) access to runner machine
diff --git a/actions/run-nextstrain-build-step/action.yaml b/actions/run-nextstrain-build-step/action.yaml
deleted file mode 100644
index f3900be..0000000
--- a/actions/run-nextstrain-build-step/action.yaml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: run-nextstrain-build-step
-description: >-
-  Runs a single `nextstrain build` command in a given sub-directory of
-  a pathogen repo. Must be provided with the name of the
-  sub-directory.
-
-inputs:
-  step:
-    description: The name of the sub-directory to run the build from
-    type: string
-    required: true
-
-runs:
-  using: "composite"
-  steps:
-    - id: run-build
-      env:
-        STEP: ${{ inputs.step }}
-      run: |
-        if [[ -f nextstrain-pathogen.yaml && -f $STEP/Snakefile && -f $STEP/build-configs/ci/config.yaml ]]; then
-          nextstrain build $STEP --configfile build-configs/ci/config.yaml
-        else
-          echo "Skipping $STEP build due to one or more missing files."
-          for i in nextstrain-pathogen.yaml $STEP/Snakefile $STEP/build-configs/ci/config.yaml; do
-            ! test -f $i && echo missing $i
-          done
-        fi
-      shell: bash
-
-    - id: upload-artifact
-      if: always()
-      uses: actions/upload-artifact@v4
-      with:
-        name: ${{inputs.step }}-outputs-${{ matrix.runtime }}
-        path: |
-          ${{ inputs.step }}/results/
-          ${{ inputs.step }}/benchmarks/
-          ${{ inputs.step }}/logs/
-          ${{ inputs.step }}/.snakemake/log/
diff --git a/actions/run-nextstrain-build/action.yaml b/actions/run-nextstrain-build/action.yaml
new file mode 100644
index 0000000..98f4614
--- /dev/null
+++ b/actions/run-nextstrain-build/action.yaml
@@ -0,0 +1,39 @@
+name: run-nextstrain-build
+description: >-
+  Runs a single `nextstrain build` command in a given sub-directory of
+  a pathogen repo. Must be provided with the name of the
+  sub-directory.
+
+inputs:
+  directory:
+    description: The name of the sub-directory to run the build from
+    type: string
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - id: run-build
+      env:
+        DIR: ${{ inputs.directory }}
+      run: |
+        if [[ -f nextstrain-pathogen.yaml && -f $DIR/Snakefile && -f $DIR/build-configs/ci/config.yaml ]]; then
+          nextstrain build $DIR --configfile build-configs/ci/config.yaml
+        else
+          echo "Skipping $DIR build due to one or more missing files."
+          for i in nextstrain-pathogen.yaml $DIR/Snakefile $DIR/build-configs/ci/config.yaml; do
+            ! test -f $i && echo missing $i
+          done
+        fi
+      shell: bash
+
+    - id: upload-artifact
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: ci-outputs-${{ inputs.directory }}-${{ inputs.runtime }}
+        path: |
+          ${{ inputs.directory }}/results/
+          ${{ inputs.directory }}/benchmarks/
+          ${{ inputs.directory }}/logs/
+          ${{ inputs.directory }}/.snakemake/log/

From 0b2029ee382f6d7f4d24aa7302bed1ad323af687 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Tue, 4 Jun 2024 10:10:49 -0700
Subject: [PATCH 05/12] Point this repo's CI back to `zika`; remove TODO
 comment [#89]

---
 .github/workflows/ci.yaml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 2d4bf65..3da7191 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -26,11 +26,7 @@ jobs:
   test-pathogen-repo-ci:
     uses: ./.github/workflows/pathogen-repo-ci.yaml
     with:
-      # XXX TODO: Revert back to nextstrain/zika (for consistency with
-      # elsewhere) once pathogen-repo-ci has support for running workflows in
-      # subdirs (i.e. for our new repo layout).
-      #   -trs, 30 Jan 2024
-      repo: nextstrain/ebola
+      repo: nextstrain/zika
       artifact-name: outputs-test-pathogen-repo-ci
     secrets: inherit
 

From e7dfc763e1296ce904c91505fccd5a6f0426e996 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Tue, 4 Jun 2024 10:13:15 -0700
Subject: [PATCH 06/12] reformat YAML for consistency, per PR feedback [#89]

---
 .github/workflows/pathogen-repo-ci.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 458baa2..5c22318 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -223,10 +223,10 @@ jobs:
         with:
           repository: ${{ inputs.repo }}
 
-      - # Need to run this after the build repo is cloned so that cloning the
-        # build repo does not overwrite the .git dir and remove the extra support files
-        # that we need from nextstrain/.github repo
-        name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
+      # Need to run this after the build repo is cloned so that cloning the
+      # build repo does not overwrite the .git dir and remove the extra support files
+      # that we need from nextstrain/.github repo
+      - name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
         uses: actions/checkout@v4
         with:
           repository: ${{ needs.workflow-context.outputs.repository }}

From a4d0d71e29265a534b64605b806588fbf1dd672f Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Tue, 4 Jun 2024 10:13:39 -0700
Subject: [PATCH 07/12] =?UTF-8?q?Update=20`run-nextstrain-build`=20`upload?=
 =?UTF-8?q?-artifact`=20step=E2=80=A6=20[#89]?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

…per PR feedback

* ignore/don't warn when no files found
* include `auspcice` directory in upload set
* sort lines
---
 actions/run-nextstrain-build/action.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/actions/run-nextstrain-build/action.yaml b/actions/run-nextstrain-build/action.yaml
index 98f4614..9c1be48 100644
--- a/actions/run-nextstrain-build/action.yaml
+++ b/actions/run-nextstrain-build/action.yaml
@@ -32,8 +32,10 @@ runs:
       uses: actions/upload-artifact@v4
       with:
         name: ci-outputs-${{ inputs.directory }}-${{ inputs.runtime }}
+        if-no-files-found: ignore
         path: |
-          ${{ inputs.directory }}/results/
+          ${{ inputs.directory }}/.snakemake/log/
+          ${{ inputs.directory }}/auspice/
           ${{ inputs.directory }}/benchmarks/
           ${{ inputs.directory }}/logs/
-          ${{ inputs.directory }}/.snakemake/log/
+          ${{ inputs.directory }}/results/

From 5e7f2cbe12febc9a43c806d6ffcb9ade01f5263f Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Tue, 4 Jun 2024 10:14:46 -0700
Subject: [PATCH 08/12] Refactor pathogen-repo-ci inputs & description, based
 on PR feedback [#89]

* Pass `runtime` as an input, rather than accessing `matrix.runtime`
  directly
* Update action description to reflect dependency on having Nextstrain
  CLI already set up via other action; add warning about the purpose
  of this action
---
 .github/workflows/pathogen-repo-ci.yaml  |  3 +++
 actions/run-nextstrain-build/action.yaml | 14 ++++++++++++--
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 5c22318..1fa7da0 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -243,13 +243,16 @@ jobs:
         uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
         with:
           directory: ingest
+          runtime: ${{ matrix.runtime }}
 
       - name: Run phylogenetic
         uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
         with:
           directory: phylogenetic
+          runtime: ${{ matrix.runtime }}
 
       - name: Run nextclade
         uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
         with:
           directory: nextclade
+          runtime: ${{ matrix.runtime }}
diff --git a/actions/run-nextstrain-build/action.yaml b/actions/run-nextstrain-build/action.yaml
index 9c1be48..32f88d0 100644
--- a/actions/run-nextstrain-build/action.yaml
+++ b/actions/run-nextstrain-build/action.yaml
@@ -1,14 +1,24 @@
 name: run-nextstrain-build
 description: >-
   Runs a single `nextstrain build` command in a given sub-directory of
-  a pathogen repo. Must be provided with the name of the
-  sub-directory.
+  a pathogen repo. Must be provided with the name of the sub-directory
+  and the runtime to use. Requires that the Nextstrain CLI runtime
+  already be provisioned (e.g., via the `setup-nextstrain-cli` action
+  in this repo).
+
+  Note that this action exists primarily as a means to keep the
+  `pathogen-repo-ci` workflow DRY; it is unlikely to be useful outside
+  the context of that specific workflow.
 
 inputs:
   directory:
     description: The name of the sub-directory to run the build from
     type: string
     required: true
+  runtime:
+    description: Nextstrain runtime to use for the build
+    type: string
+    required: true
 
 runs:
   using: "composite"

From b58836f5bee190f76d763e21076334818579216a Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Tue, 4 Jun 2024 10:22:03 -0700
Subject: [PATCH 09/12] `mv actions/run-nextstrain-build
 actions/run-nextstrain-ci-build` [#89]

---
 .github/workflows/pathogen-repo-ci.yaml                     | 6 +++---
 README.md                                                   | 2 +-
 .../action.yaml                                             | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename actions/{run-nextstrain-build => run-nextstrain-ci-build}/action.yaml (98%)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 1fa7da0..7926a68 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -240,19 +240,19 @@ jobs:
           runtime: ${{ matrix.runtime }}
 
       - name: Run ingest
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
         with:
           directory: ingest
           runtime: ${{ matrix.runtime }}
 
       - name: Run phylogenetic
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
         with:
           directory: phylogenetic
           runtime: ${{ matrix.runtime }}
 
       - name: Run nextclade
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-build
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
         with:
           directory: nextclade
           runtime: ${{ matrix.runtime }}
diff --git a/README.md b/README.md
index cb31d92..b9a506a 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ See also GitHub's [documentation on issue and PR templates](https://docs.github.
 
 Invoked by our GitHub Actions workflows, including the reusable workflows below.
 
-- [Run Nextstrain Build](actions/run-nextstrain-build/action.yaml)
+- [Run Nextstrain CI Build](actions/run-nextstrain-ci-build/action.yaml)
 - [Setup Nextstrain CLI](actions/setup-nextstrain-cli/action.yaml)
 - [shellcheck](actions/shellcheck/action.yaml)
 - [Setup SSH](actions/setup-ssh/action.yaml) access to runner machine
diff --git a/actions/run-nextstrain-build/action.yaml b/actions/run-nextstrain-ci-build/action.yaml
similarity index 98%
rename from actions/run-nextstrain-build/action.yaml
rename to actions/run-nextstrain-ci-build/action.yaml
index 32f88d0..66f35be 100644
--- a/actions/run-nextstrain-build/action.yaml
+++ b/actions/run-nextstrain-ci-build/action.yaml
@@ -1,4 +1,4 @@
-name: run-nextstrain-build
+name: run-nextstrain-ci-build
 description: >-
   Runs a single `nextstrain build` command in a given sub-directory of
   a pathogen repo. Must be provided with the name of the sub-directory

From 2687ba0b7e4e816de819ca5ba14742e0a7e90062 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Wed, 5 Jun 2024 10:39:56 -0700
Subject: [PATCH 10/12] Set nextstrain runtime, per PR feedback [#89]

---
 actions/run-nextstrain-ci-build/action.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/actions/run-nextstrain-ci-build/action.yaml b/actions/run-nextstrain-ci-build/action.yaml
index 66f35be..8d8e0b4 100644
--- a/actions/run-nextstrain-ci-build/action.yaml
+++ b/actions/run-nextstrain-ci-build/action.yaml
@@ -28,6 +28,7 @@ runs:
         DIR: ${{ inputs.directory }}
       run: |
         if [[ -f nextstrain-pathogen.yaml && -f $DIR/Snakefile && -f $DIR/build-configs/ci/config.yaml ]]; then
+          nextstrain check-setup ${{ inputs.runtime }} --set-default
           nextstrain build $DIR --configfile build-configs/ci/config.yaml
         else
           echo "Skipping $DIR build due to one or more missing files."

From 46abc25ddbc494b7b9a6e52d4dcac6d24e79ddb0 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 7 Jun 2024 11:29:22 -0700
Subject: [PATCH 11/12] shell linting-ish fixes, from PR review [#89]

---
 actions/run-nextstrain-ci-build/action.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/actions/run-nextstrain-ci-build/action.yaml b/actions/run-nextstrain-ci-build/action.yaml
index 8d8e0b4..0c2e115 100644
--- a/actions/run-nextstrain-ci-build/action.yaml
+++ b/actions/run-nextstrain-ci-build/action.yaml
@@ -27,13 +27,13 @@ runs:
       env:
         DIR: ${{ inputs.directory }}
       run: |
-        if [[ -f nextstrain-pathogen.yaml && -f $DIR/Snakefile && -f $DIR/build-configs/ci/config.yaml ]]; then
+        if [[ -f nextstrain-pathogen.yaml && -f "$DIR"/Snakefile && -f "$DIR"/build-configs/ci/config.yaml ]]; then
           nextstrain check-setup ${{ inputs.runtime }} --set-default
-          nextstrain build $DIR --configfile build-configs/ci/config.yaml
+          nextstrain build "$DIR" --configfile build-configs/ci/config.yaml
         else
           echo "Skipping $DIR build due to one or more missing files."
-          for i in nextstrain-pathogen.yaml $DIR/Snakefile $DIR/build-configs/ci/config.yaml; do
-            ! test -f $i && echo missing $i
+          for i in nextstrain-pathogen.yaml "$DIR"/Snakefile "$DIR"/build-configs/ci/config.yaml; do
+            [[ -f $i ]] || echo missing $i
           done
         fi
       shell: bash

From 3b4969271d099dcb8cec364aecf98a9da29260bb Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 7 Jun 2024 11:39:32 -0700
Subject: [PATCH 12/12] Restore `artifact-name` functionality, per PR feedback
 [#89]

* Update `artifact-name` description in `pathogen-repo-ci.yaml` to
  make it clear build directory will be appended to provided value,
  and to update default value to make clear these are CI results
* Pass `artifact-name` down into `run-nextstrain-ci-build` steps ni
  `pathogen-repo-ci` workflow
* Add `artifact-name` input to `run-nextstrain-ci-build` action and
  use it in `upload-artifact` action step
---
 .github/workflows/pathogen-repo-ci.yaml     | 22 ++++++++++++++-------
 actions/run-nextstrain-ci-build/action.yaml |  8 +++++++-
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 7926a68..71149f9 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -74,15 +74,20 @@ on:
 
       artifact-name:
         description: >-
-          Name to use for build results artifact uploaded at the end of the
-          workflow.  This name will be suffixed with other information from the
-          workflow job matrix to distinguish each artifact in a workflow run.
+          A base name to use for the uploaded artifacts from the
+          build. This will be concatenated with the directory name
+          used to invoke the build to generate the full artifact file
+          name.
 
-          If you're invoking this workflow multiple times from the same calling
-          workflow, you should set this.  Otherwise, the default of "outputs"
-          is probably fine.
+          Defaults to `ci-outputs`.
+
+          N.b., you almost certainly don't need to change this, unless
+          you're running multiple invocations of this action in a
+          single workflow. Then you should provide unique values to
+          ensure you can access the artifacts from all the builds
+          you're doing.
         type: string
-        default: outputs
+        default: ci-outputs
         required: false
 
       continue-on-error:
@@ -244,15 +249,18 @@ jobs:
         with:
           directory: ingest
           runtime: ${{ matrix.runtime }}
+          artifact-name: ${{ inputs.artifact-name }}
 
       - name: Run phylogenetic
         uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
         with:
           directory: phylogenetic
           runtime: ${{ matrix.runtime }}
+          artifact-name: ${{ inputs.artifact-name }}
 
       - name: Run nextclade
         uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
         with:
           directory: nextclade
           runtime: ${{ matrix.runtime }}
+          artifact-name: ${{ inputs.artifact-name }}
diff --git a/actions/run-nextstrain-ci-build/action.yaml b/actions/run-nextstrain-ci-build/action.yaml
index 0c2e115..66cf141 100644
--- a/actions/run-nextstrain-ci-build/action.yaml
+++ b/actions/run-nextstrain-ci-build/action.yaml
@@ -11,6 +11,12 @@ description: >-
   the context of that specific workflow.
 
 inputs:
+  artifact-name:
+    description: >-
+      Name to append to the build directory to generate a
+      unique artifact name for the upload action.
+    type: string
+    required: true
   directory:
     description: The name of the sub-directory to run the build from
     type: string
@@ -42,7 +48,7 @@ runs:
       if: always()
       uses: actions/upload-artifact@v4
       with:
-        name: ci-outputs-${{ inputs.directory }}-${{ inputs.runtime }}
+        name: ${{ inputs.artifact-name }}-${{ inputs.directory }}-${{ inputs.runtime }}
         if-no-files-found: ignore
         path: |
           ${{ inputs.directory }}/.snakemake/log/