Merge pull request #219 from qbic-pipelines/dev

Release 2.2
qbic-pipelines · Aug 21, 2023 · f5e54b6 · f5e54b6
2 parents 64f7f63 + c30e7eb
commit f5e54b6
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diff --git a/.editorconfig b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,9 +1,9 @@
 # qbic-pipelines/rnadeseq: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/rnadeseq.
+Many thanks for taking an interest in improving qbic-pipelines/rnadeseq.
 
-We try to manage the required tasks for nf-core/rnadeseq using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for qbic-pipelines/rnadeseq using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
@@ -13,8 +13,8 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for qbic-pipelines/rnadeseq, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/rnadeseq issues](https://github.com/nf-core/rnadeseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/rnadeseq repository](https://github.com/nf-core/rnadeseq) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [qbic-pipelines/rnadeseq issues](https://github.com/qbic-pipelines/rnadeseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [qbic-pipelines/rnadeseq repository](https://github.com/qbic-pipelines/rnadeseq) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -99,3 +99,18 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/qbic-pipelines/rnadeseq/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -27,6 +27,8 @@ body:
       placeholder: |
         $ nextflow run ...
 
+        Some output where something broke
+
   - type: textarea
     id: files
     attributes:
@@ -40,9 +42,9 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of qbic-pipelines/rnadeseq _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/rnadeseq pipeline
+description: Suggest an idea for the qbic-pipelines/rnadeseq pipeline
 labels: enhancement
 body:
   - type: textarea

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/qbic-pipelin
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnadeseq/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/rnadeseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/qbic-pipelines/rnadeseq/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -14,20 +14,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnadeseq/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnadeseq/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
+          profiles: test_full
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -12,17 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnadeseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnadeseq/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
+          profiles: test
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -12,6 +12,10 @@ env:
   NXF_ANSI_LOG: false
   CAPSULE_LOG: none
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Run pipeline with test data
@@ -22,11 +26,11 @@ jobs:
       matrix:
         # Nextflow versions
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Check if Dockerfile or Conda environment changed
         uses: technote-space/get-diff-action@v4
@@ -36,13 +40,14 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
+        run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2
 
+      # Change the version above and the third version below before/after release
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
-          docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
+          docker pull ghcr.io/qbic-pipelines/rnadeseq:dev
+          docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -56,7 +61,7 @@ jobs:
     name: Test workflow parameters
     runs-on: ubuntu-latest
     env:
-      NXF_VER: "22.10.1"
+      NXF_VER: "23.04.0"
       NXF_ANSI_LOG: false
     strategy:
       # This tells github to continue running other profile tests if some tests fail (default cancels all tests upon failure)
@@ -70,6 +75,7 @@ jobs:
             "test_contrast_list",
             "test_no_multiqc",
             "test_relevel",
+            "test_smrnaseq",
             "test_star_rsem",
             "test_star_salmon",
             "test_use_vst",
@@ -78,7 +84,7 @@ jobs:
           ]
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Check if Dockerfile or Conda environment changed
         uses: technote-space/get-diff-action@v4
@@ -88,13 +94,14 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
+        run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2
 
+      # Change the version above and the third version below before/after release
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
-          docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
+          docker pull ghcr.io/qbic-pipelines/rnadeseq:dev
+          docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies

diff --git a/.github/workflows/push_dockerhub.yml b/.github/workflows/push_dockerhub.yml
diff --git a/.github/workflows/push_github_container_reg.yml b/.github/workflows/push_github_container_reg.yml
@@ -0,0 +1,38 @@
+name: Docker push
+# This builds the docker image and pushes it to GHCR
+# Runs on qbic-pipelines repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+  release:
+    types: [published]
+
+jobs:
+  push_github:
+    name: Push new Docker image to GHCR
+    runs-on: ubuntu-latest
+    # Only run for the qbic-pipelines repo, for releases and merged PRs
+    if: ${{ github.repository == 'qbic-pipelines/rnadeseq' }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:latest
+
+      - name: Log in to registry
+        # Update the personal access token to GITHUB_TOKEN
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u $ --password-stdin
+
+      - name: Push image to GHCR (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rnadeseq:latest ghcr.io/qbic-pipelines/rnadeseq:dev
+          docker push ghcr.io/qbic-pipelines/rnadeseq:dev
+
+      - name: Push image to GHCR (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rnadeseq:latest ghcr.io/qbic-pipelines/rnadeseq:${{ github.event.release.tag_name }}
+          docker push ghcr.io/qbic-pipelines/rnadeseq:${{ github.event.release.tag_name }}
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,3 +1,5 @@
+repository_type: pipeline
+
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
@@ -18,7 +20,6 @@ lint:
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awsfulltest.yml
     - .github/workflows/awstest.yml
-    - .github/workflows/push_dockerhub.yml
     - assets/multiqc_config.yaml
     - assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
     - bin/markdown_to_html.r
@@ -35,5 +36,3 @@ lint:
 
   multiqc_config:
     - report_comment # otherwise throws error: multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.                                                                           │
-
-repository_type: pipeline
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier