The Big Merge

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // 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"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}

.gitattributes

@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -1,22 +1,20 @@
-# nf-core/treeval: Contributing Guidelines
+# sanger-tol/treeval: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/treeval.
+Many thanks for taking an interest in improving sanger-tol/treeval.
 
-We try to manage the required tasks for nf-core/treeval using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for sanger-tol/treeval 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 ;)
 
-> If you need help using or modifying nf-core/treeval then the best place to ask is on the nf-core Slack [#treeval](https://nfcore.slack.com/channels/treeval) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/treeval, the standard workflow is as follows:
+If you'd like to write some code for sanger-tol/treeval, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/treeval issues](https://github.com/nf-core/treeval/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/treeval repository](https://github.com/nf-core/treeval) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [sanger-tol/treeval issues](https://github.com/sanger-tol/treeval/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 [sanger-tol/treeval repository](https://github.com/sanger-tol/treeval) 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
@@ -52,13 +50,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - A PR should be made on `master` from patch to directly this particular bug.
 
-## Getting help
-
-For further information/help, please consult the [nf-core/treeval documentation](https://nf-co.re/treeval/usage) and don't hesitate to get in touch on the nf-core Slack [#treeval](https://nfcore.slack.com/channels/treeval) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
 ## Pipeline contribution conventions
 
-To make the nf-core/treeval 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 sanger-tol/treeval 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
 
@@ -101,3 +95,19 @@ 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/sanger-tol/treeval/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,49 +2,53 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-  - type: markdown
-    attributes:
-      value: |
-        Before you post this issue, please check the documentation:
-
-        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/treeval pipeline documentation](https://nf-co.re/treeval/usage)
-
   - type: textarea
     id: description
     attributes:
       label: Description of the bug
       description: A clear and concise description of what the bug is.
     validations:
       required: true
-
   - type: textarea
     id: command_used
     attributes:
       label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
       render: console
-      placeholder: |
-        $ nextflow run ...
+      placeholder: "$ nextflow run ...
+
 
         Some output where something broke
 
+        "
   - type: textarea
     id: files
     attributes:
       label: Relevant files
-      description: |
-        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
-        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
 
+        "
   - type: textarea
     id: system
     attributes:
       label: System information
-      description: |
-        * Nextflow version _(eg. 21.10.3)_
+      description: "* Nextflow version _(eg. 22.10.1)_
+
         * 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 nf-core/treeval _(eg. 1.1, 1.5, 1.8.2)_
+
+        * Version of sanger-tol/treeval _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.github/ISSUE_TEMPLATE/config.yml

@@ -4,4 +4,4 @@ contact_links:
     about: Please join the nf-core community here
   - name: "Slack #treeval channel"
     url: https://nfcore.slack.com/channels/treeval
-    about: Discussion about the nf-core/treeval pipeline
+    about: Discussion about the sanger-tol/treeval pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/treeval pipeline
+description: Suggest an idea for the sanger-tol/treeval pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,21 @@
 <!--
-# nf-core/treeval pull request
+# sanger-tol/treeval pull request
 
-Many thanks for contributing to nf-core/treeval!
+Many thanks for contributing to sanger-tol/treeval!
 
 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/nf-core/treeval/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/treeval/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/nf-core/treeval/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/treeval _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/sanger-tol/treeval/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.

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ 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 == 'nf-core/treeval'
+        if: github.repository == 'sanger-tol/treeval'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/treeval ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/treeval ]] && [[ $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

.github/workflows/ci.yml

@@ -10,41 +10,42 @@ on:
 
 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
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/treeval') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/treeval') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Nextflow versions
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "22.10.1"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Download test data
+        # Download A fungal test data set that is full enough to show some real output.
+        run: |
+          curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -
+
+      - name: Run RAPID pipeline with test data
+        # Remember that you can parallelise this by using strategy.matrix
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+          nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile test_github,docker --outdir ./results-rapid
 
-      - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
+      - name: Run FULL pipeline with test data
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test_github,docker --outdir ./results-full

.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 }}"

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/treeval'
+      github.repository == 'sanger-tol/treeval'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'