Renaming things per PR feedback [#89]

* run-nextstrain-build-step -> run-nextstrain-build
* inputs.step -> inputs.directory

.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

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

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/