Add a Github Action Workflow to the pipeline template that tests a su…

…ccessful download.

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nf-core/tools: Changelog
 
+# v2.12.0dev
+
+### Template
+
+- Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download'
+
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 
 ### Template

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -0,0 +1,70 @@
+name: Test successful pipeline download with 'nf-core download'
+
+# Run the workflow when:
+#  - dispatched manually
+#  - when a PR is opened or reopened to dev or master branches
+#  - the head branch of the pull request is updated. (Do we need this?)
+
+on:
+  workflow_dispatch:
+  pull_request:
+    types:
+      - opened
+    branches:
+      - master
+      - dev
+  #pull_request_target:
+  #  branches:
+  #    - master
+  #    - dev
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  download:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          architecture: "x64"
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install git+https://github.com/nf-core/tools.git@dev
+
+      - name: Get the repository name and current branch set as environment variable
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
+          echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
+
+      - name: Download the pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+        run: |
+          nf-core download ${{ env.REPO_LOWERCASE }} \
+          --revision ${{ env.REPO_BRANCH }} \
+          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          --compress "none" \
+          --container-system 'singularity' \
+          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-cache-utilisation 'amend' \
+          --download-configuration
+
+      - name: Inspect download
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+
+      - name: Run the downloaded pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results