Merge pull request #12 from nf-cmgg/template-update-2.13.1

Template update 2.13.1

.devcontainer/devcontainer.json

@@ -2,22 +2,15 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

.editorconfig

@@ -18,7 +18,20 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py,md}]
+indent_style = unset

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Contributing Guidelines
+# nf-cmgg/wisecondorx: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx.
+Many thanks for taking an interest in improving nf-cmgg/wisecondorx.
 
-We try to manage the required tasks for CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-cmgg/wisecondorx 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!
 Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx, the standard workflow is as follows:
+If you'd like to write some code for nf-cmgg/wisecondorx, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx issues](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/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 [CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx repository](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-cmgg/wisecondorx issues](https://github.com/nf-cmgg/wisecondorx/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-cmgg/wisecondorx repository](https://github.com/nf-cmgg/wisecondorx) 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
@@ -23,6 +23,12 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
@@ -52,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the nf-cmgg/wisecondorx code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -79,7 +85,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 
@@ -102,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/codespaces)
+- Open the repo in [Codespaces](https://github.com/nf-cmgg/wisecondorx/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,7 +38,7 @@ body:
     id: system
     attributes:
       label: System information
-      description: "* Nextflow version _(eg. 22.10.1)_
+      description: "* Nextflow version _(eg. 23.04.0)_
 
         * Hardware _(eg. HPC, Desktop, Cloud)_
 
@@ -49,7 +49,6 @@ body:
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
-        * Version of CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx _(eg. 1.1, 1.5,
-        1.8.2)_
+        * Version of nf-cmgg/wisecondorx _(eg. 1.1, 1.5, 1.8.2)_
 
         "

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pipeline
+description: Suggest an idea for the nf-cmgg/wisecondorx pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,23 +1,24 @@
 <!--
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pull request
+# nf-cmgg/wisecondorx pull request
 
-Many thanks for contributing to CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx!
+Many thanks for contributing to nf-cmgg/wisecondorx!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/wisecondorx/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] 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/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/wisecondorx/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>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/branch.yml

@@ -11,15 +11,15 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx'
+        if: github.repository == 'nf-cmgg/wisecondorx'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-cmgg/wisecondorx ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/ci.yml

@@ -19,16 +19,16 @@ jobs:
   test:
     name: Run nf-test with Nextflow version ${{ matrix.NXF_VER }}
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/wisecondorx') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -39,6 +39,9 @@ jobs:
         run: |
           conda install -c bioconda nf-test
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run pipeline with test data
         run: |
           $CONDA/bin/nf-test test --junitxml=default.xml

.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@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+        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 }}"

.github/workflows/download_pipeline.yml

@@ -0,0 +1,72 @@
+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:
+    inputs:
+      testbranch:
+        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        required: true
+        default: "dev"
+  pull_request:
+    types:
+      - opened
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # 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.event.inputs.testbranch || 'dev' }}" >> ${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