CCBR · kelly-sovacool · Feb 9, 2026 · Feb 9, 2026 · Feb 9, 2026 · Feb 9, 2026
@@ -1,8 +1,8 @@
 * @kelly-sovacool
 /.github/ @kelly-sovacool
-/docs/lucidcharts* @kopardev
-/docs/conda-mamba/conda-to-mamba @kopardev
 /docs/HPCDME  @kopardev
 /docs/UCSC  @kopardev
-/docs/github/guide @kopardev
+/docs/conda-mamba/conda-to-mamba @kopardev
 /docs/generative-AI/copilot-cli.md @kopardev
+/docs/github/guide @kopardev
+/docs/lucidcharts* @kopardev
@@ -0,0 +1,48 @@
+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 existing Issues and Discussions to see if your problem has already been reported or solved. If you are unsure, please ask in the [CHAMPAGNE forum](https://forum.ccbr.medschl.cam.ac.uk/c/champagne) for help.
+
+  - 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.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop any 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.
+        If the bug is related to a GUI, add screenshots to help explain your problem.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity)_
+        * OS _(eg. Ubuntu Linux, macOS)_
+        * Version of CCBR/CHAMPAGNE _(eg. 1.0, 1.8.2)_
@@ -0,0 +1,4 @@
+contact_links:
+  - name: Discussions
+    url: https://github.com/CCBR/HowTos/discussions
+    about: Please ask and answer questions here.
@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. Before submitting, please check if there is already an open issue for the same feature.
+    validations:
+      required: true
@@ -1,7 +1,8 @@
 ## HowTos development version
 
-- Publishing Shiny apps to NCI's Posit Connect servers (#53, @escauley)
+- New guide: Publishing Shiny apps to NCI's Posit Connect servers (#53, @escauley)
 - Update the Zenodo guide with current CCBR practices (#55, @kelly-sovacool)
+- Create an overview of authentication with GitHub, a guide on using SSH keys with GitHub, and how to use fine-grained tokens. (#61, @kelly-sovacool)
 
 ## HowTos 1.0.0
 

@@ -0,0 +1,9 @@
+---
+title: Authentication with GitHub
+date: 2026-02-09
+---
+
+- [SSH Keys](./ssh-keys/) - **recommend** for running git commands from the terminal
+- [GitHub Apps](https://ccbr.github.io/actions/gh-app-auth.html) - for GitHub Actions and other automation platforms
+- [Fine-grained tokens](./tokens/fine-grained.qmd) - needed for **Code Ocean** and other platforms requiring a token
+- [Classic tokens](./tokens/classic.qmd) - no longer in use as of March 1st, 2026