Merge branch 'dev' into update-image-syntax-in-template

.github/workflows/fix-linting.yml

@@ -17,6 +17,13 @@ jobs:
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
@@ -34,9 +41,21 @@ jobs:
         run: pip install pre-commit
 
       - name: Run pre-commit
+        id: pre-commit
         run: pre-commit run --all-files
+        continue-on-error: true
+
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: ${{ steps.pre-commit.outcome }} == 'success'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: green_check_mark
 
       - name: Commit & push changes
+        id: commit-and-push
+        if: ${{ steps.pre-commit.outcome }} == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
@@ -45,3 +64,19 @@ jobs:
           git status
           git commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        if: ${{ steps.commit-and-push.outcome }} == 'success'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: pencil2
+
+      - name: react if linting errors were not fixed
+        if: ${{ steps.commit-and-push.outcome }} == 'failure'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: x
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.

.gitpod.yml

@@ -10,11 +10,6 @@ tasks:
     command: |
       unset JAVA_TOOL_OPTIONS
 
-  - name: Use pdiff for nf-test diff viewing
-    command: |
-      export NFT_DIFF="pdiff"
-      export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
-
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

CHANGELOG.md

@@ -4,9 +4,11 @@
 
 ### Template
 
+- Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download' ([#2618](https://github.com/nf-core/tools/pull/2618))
 - Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
 - Use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640))
 - switch to new image syntax in readme ([#2645](https://github.com/nf-core/tools/pull/2645))
+- Add conda channel order to nextflow.config ([#2094](https://github.com/nf-core/tools/pull/2094))
 
 ### Download
 
@@ -23,6 +25,7 @@
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630))
 - Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632))
 - update python image version in docker file ([#2636](https://github.com/nf-core/tools/pull/2636))
+- Set pdiff as nf-test differ in Docker image for Gitpod ([#2642](https://github.com/nf-core/tools/pull/2642))
 
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 

nf_core/gitpod/gitpod.Dockerfile

@@ -62,4 +62,8 @@ RUN conda config --add channels defaults && \
 RUN nextflow self-update
 
 # Install nf-core
-RUN python -m pip install .
+RUN python -m pip install . --no-cache-dir
+
+# Setup pdiff for nf-test diffs
+RUN export NFT_DIFF="pdiff" && \
+    export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"

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

@@ -0,0 +1,68 @@
+name: Test successful pipeline download with 'nf-core download'
+
+# Run the workflow when:
+#  - dispatched manually
+#  - when a PR is opened or reopened to master branch
+#  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
+
+on:
+  workflow_dispatch:
+  pull_request:
+    types:
+      - opened
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  download:
+    runs-on: ["self-hosted"]
+    steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          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

nf_core/pipeline-template/.gitpod.yml

@@ -7,10 +7,7 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
-  - name: Use pdiff for nf-test diff viewing
-    command: |
-      export NFT_DIFF="pdiff"
-      export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

nf_core/pipeline-template/nextflow.config

@@ -100,6 +100,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        channels               = ['conda-forge', 'bioconda', 'defaults']
         apptainer.enabled      = false
     }
     mamba {