refactor: Update TEMPLATE branch

.devcontainer/devcontainer.json

@@ -1,20 +1,20 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // 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"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // 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"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.github/CONTRIBUTING.md

@@ -1,23 +1,20 @@
-# `nf-core/postprocessing`: Contributing Guidelines
+# `Clinical-Genomics/oncorefiner`: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/postprocessing.
+Many thanks for taking an interest in improving Clinical-Genomics/oncorefiner.
 
-We try to manage the required tasks for nf-core/postprocessing using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for Clinical-Genomics/oncorefiner 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 ;)
 
-> [!NOTE]
-> If you need help using or modifying nf-core/postprocessing then the best place to ask is on the nf-core Slack [#postprocessing](https://nfcore.slack.com/channels/postprocessing) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/postprocessing, the standard workflow is as follows:
+If you'd like to write some code for Clinical-Genomics/oncorefiner, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/postprocessing issues](https://github.com/nf-core/postprocessing/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/postprocessing repository](https://github.com/nf-core/postprocessing) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [Clinical-Genomics/oncorefiner issues](https://github.com/Clinical-Genomics/oncorefiner/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 [Clinical-Genomics/oncorefiner repository](https://github.com/Clinical-Genomics/oncorefiner) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines 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
@@ -59,13 +56,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - Open a pull-request from `patch` to `main`/`master` with the changes.
 
-## Getting help
-
-For further information/help, please consult the [nf-core/postprocessing documentation](https://nf-co.re/postprocessing/usage) and don't hesitate to get in touch on the nf-core Slack [#postprocessing](https://nfcore.slack.com/channels/postprocessing) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
 ## Pipeline contribution conventions
 
-To make the `nf-core/postprocessing` 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 `Clinical-Genomics/oncorefiner` 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
 
@@ -78,7 +71,7 @@ If you wish to contribute a new step, please use the following coding standards:
 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+8. If applicable, add a new test in the `tests` directory.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
@@ -115,7 +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/nf-core/postprocessing/codespaces)
+- Open the repo in [Codespaces](https://github.com/Clinical-Genomics/oncorefiner/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,13 +2,6 @@ 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/postprocessing pipeline documentation](https://nf-co.re/postprocessing/usage)
   - type: textarea
     id: description
     attributes:
@@ -46,4 +39,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/postprocessing _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of Clinical-Genomics/oncorefiner _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,7 +1 @@
-contact_links:
-  - name: Join nf-core
-    url: https://nf-co.re/join
-    about: Please join the nf-core community here
-  - name: "Slack #postprocessing channel"
-    url: https://nfcore.slack.com/channels/postprocessing
-    about: Discussion about the nf-core/postprocessing pipeline
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/postprocessing pipeline
+description: Suggest an idea for the Clinical-Genomics/oncorefiner pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,21 @@
 <!--
-# nf-core/postprocessing pull request
+# Clinical-Genomics/oncorefiner pull request
 
-Many thanks for contributing to nf-core/postprocessing!
+Many thanks for contributing to Clinical-Genomics/oncorefiner!
 
 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/postprocessing/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/Clinical-Genomics/oncorefiner/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/postprocessing/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/postprocessing _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/Clinical-Genomics/oncorefiner/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/branch.yml

@@ -13,9 +13,9 @@ jobs:
     steps:
       # PRs to the nf-core repo main/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/postprocessing'
+        if: github.repository == 'Clinical-Genomics/oncorefiner'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/postprocessing ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == Clinical-Genomics/oncorefiner ]] && [[ $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/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         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."