Merge branch 'MultiQC:main' into main

Author: caruizelembioinfo

.claude/skills/triaging-module-requests/analysis-templates.md

@@ -180,7 +180,7 @@ Our records show that [Tool Name] might already have a MultiQC module:
 - Module: `multiqc.modules.[module_name]`
 - Documentation: [Link]
 
-Please check the [list of existing modules](https://multiqc.info/modules/) before proceeding. If the existing module doesn't meet your needs, please explain what additional functionality you require.
+Please check the [list of existing modules](https://docs.seqera.io/multiqc/modules/) before proceeding. If the existing module doesn't meet your needs, please explain what additional functionality you require.
 ```
 
 ## General Guidelines

.github/ISSUE_TEMPLATE/module-request.yml

@@ -115,6 +115,6 @@ body:
       description: These help improve your request's priority, but aren't strictly required. We're here to help!
       options:
         - label: I have included example data files (uploaded/zipped, not copy-pasted)
-        - label: I have checked that no similar module already exists in the [MultiQC modules list](https://multiqc.info/modules/)
+        - label: I have checked that no similar module already exists in the [MultiQC modules list](https://docs.seqera.io/multiqc/modules/)
         - label: I have provided the tool's homepage or repository URL
         - label: I understand this request will be prioritized based on tool popularity, community need, and request quality

.github/workflows/claude-code-review.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      pull-requests: read
+      pull-requests: write
       issues: read
       id-token: write
 
@@ -51,6 +51,7 @@ jobs:
           PR_NUMBER: ${{ steps.pr-info.outputs.pr_number }}
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+          allowed_non_write_users: "*"
           show_full_output: true
           prompt: |
             Please review pull request #${{ steps.pr-info.outputs.pr_number }} and provide feedback on:

README.md

@@ -8,7 +8,7 @@
 
 ### Aggregate bioinformatics results across many samples into a single report
 
-##### Find [documentation](https://docs.seqera.io/multiqc) and [example reports](https://multiqc.info/example-reports/) at [http://multiqc.info](http://multiqc.info)
+##### Find [documentation](https://docs.seqera.io/multiqc) and [example reports](https://seqera.io/multiqc/#reports) at [https://seqera.io/multiqc/](https://seqera.io/multiqc/)
 
 [![PyPI Version](https://img.shields.io/pypi/v/multiqc)](https://pypi.python.org/pypi/multiqc/)
 [![Bioconda Version](https://img.shields.io/conda/v/bioconda/multiqc?label=bioconda)](https://bioconda.github.io/recipes/multiqc/README.html)
@@ -32,28 +32,37 @@ More modules are being written all the time. Please suggest any ideas as a new
 
 ## Installation
 
-You can install MultiQC from [PyPI](https://pypi.python.org/pypi/multiqc/)
-using `pip` as follows:
+You can install MultiQC using [uv](https://docs.astral.sh/uv/) (no separate Python installation required):
+
+```bash
+uv tool install multiqc
+```
+
+Alternatively, install from [PyPI](https://pypi.python.org/pypi/multiqc/) using `pip`:
 
 ```bash
 pip install multiqc
 ```
 
-Alternatively, you can install using [Conda](http://anaconda.org/)
+Or install using [Conda](http://anaconda.org/)
 from [Bioconda](https://bioconda.github.io/) ([set up your channels](https://bioconda.github.io/#usage) first):
 
 ```bash
 conda install multiqc
 ```
 
-If you would like the development version from GitHub instead, you can install it with `pip`:
+If you would like the development version from GitHub instead, you can install it with `uv` or `pip`:
+
+```bash
+uv tool install git+https://github.com/MultiQC/MultiQC.git
+```
 
 ```bash
 pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git
 ```
 
 MultiQC is also available via Docker and Singularity images, Galaxy wrappers, and
-many more software distribution systems.
+many more distribution methods.
 See [the documentation](https://docs.seqera.io/multiqc/getting_started/installation/) for details.
 
 ## Usage

docs/markdown/getting_started/installation.md

@@ -12,7 +12,7 @@ If you're new to software packaging, this page can be a little overwhelming.
 If in doubt, a general rule is:
 
 - _Running MultiQC in a pipeline?_   Use [Docker](#docker) or [Singularity](#singularity).
-- _Running MultiQC locally?_   Use [Pip](#pip--pypi) or [Conda](#conda).
+- _Running MultiQC locally?_   Use [uv](#uv), [Pip](#pip--pypi), or [Conda](#conda).
 
 :::tip{title="Installation cheat sheet"}
 
@@ -21,19 +21,19 @@ Know what you're doing with this kind of thing? Here's a quick reference:
 <table><thead>
 <tr><th>Method</th><th>Command</th></tr>
 </thead><tbody><tr>
-<td>Pip</td>
+<td>uv</td>
 <td>
 
 ```bash
-pip install multiqc
+uv tool install multiqc
 ```
 
 </td></tr><tr>
-<td>Pip (dev version)</td>
+<td>Pip</td>
 <td>
 
 ```bash
-pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git
+pip install multiqc
 ```
 
 </td></tr><tr>
@@ -44,6 +44,22 @@ pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.g
 conda install multiqc
 ```
 
+</td></tr><tr>
+<td>uv (dev version)</td>
+<td>
+
+```bash
+uv tool install git+https://github.com/MultiQC/MultiQC.git
+```
+
+</td></tr><tr>
+<td>Pip (dev version)</td>
+<td>
+
+```bash
+pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git
+```
+
 </td></tr><tr>
 <td>Docker</td>
 <td>
@@ -63,6 +79,10 @@ MultiQC is written in Python and needs a Python installation to run.
 To run MultiQC manually install, you'll typically install it into a local Python environment.
 MultiQC requires Python version 3.9 or above.
 
+:::tip
+If you use [uv](#uv) to install MultiQC, you don't need to install Python separately — uv automatically downloads and manages Python for you.
+:::
+
 ### System Python
 
 Python comes installed on most operating systems. You can install MultiQC directly here, but it is _not_ recommended. This often causes problems, and it's a little risky to mess with it.
@@ -71,6 +91,28 @@ Python comes installed on most operating systems. You can install MultiQC direct
 If you find yourself prepending `sudo` to any MultiQC commands, take a step back and think about Python virtual environments / conda instead.
 :::
 
+### Python with uv
+
+[uv](https://docs.astral.sh/uv/) is a fast Python package and project manager that can also install and manage Python versions.
+If you don't have Python installed, uv will automatically download it when needed — no separate Python installation required.
+
+To install uv:
+
+```bash
+# macOS / Linux
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Windows
+powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
+```
+
+uv will automatically download a suitable Python version when you install or run a Python package.
+If you'd like to install a specific Python version explicitly, you can do so with:
+
+```bash
+uv python install 3.13
+```
+
 ### Python with Conda
 
 To see if you have python installed, run `python --version` on the command line.
@@ -108,6 +150,62 @@ python3 -m multiqc .
 
 There are a few different ways to install MultiQC into your local Python environment:
 
+### uv
+
+[uv](https://docs.astral.sh/uv/) is a fast Python package and project manager, written in Rust.
+It can replace pip, pip-tools, pipx, pyenv, and virtualenv — all in a single tool.
+uv automatically manages Python installations, so you don't need to install Python separately.
+
+The recommended way to install MultiQC with uv is as a tool:
+
+```bash
+uv tool install multiqc
+```
+
+This installs MultiQC into an isolated environment and adds the `multiqc` command to your PATH.
+You can then run `multiqc` directly:
+
+```bash
+multiqc .
+```
+
+Alternatively, you can run MultiQC without installing it permanently using `uvx` (an alias for `uv tool run`):
+
+```bash
+uvx multiqc .
+```
+
+To upgrade MultiQC:
+
+```bash
+uv tool upgrade multiqc
+```
+
+#### Development version
+
+If you would like the development version from GitHub instead:
+
+```bash
+uv tool install git+https://github.com/MultiQC/MultiQC.git
+```
+
+To update the dev version between releases, use `--reinstall`:
+
+```bash
+uv tool install --reinstall git+https://github.com/MultiQC/MultiQC.git
+```
+
+You can also run the dev version directly without installing, using `uvx`:
+
+```bash
+uvx --from git+https://github.com/MultiQC/MultiQC.git multiqc .
+```
+
+:::tip
+uv can also be used as a drop-in replacement for pip inside virtual environments.
+See the [uv documentation](https://docs.astral.sh/uv/) for more details.
+:::
+
 ### Conda
 
 MultiQC is available on [Bioconda](https://bioconda.github.io/).
@@ -134,7 +232,7 @@ Doing so will likely cause weird stuff to happen (such as only being able to ins
 
 ### Pip / PyPI
 
-This is the easiest way to install MultiQC. `pip` is the package manager for the Python Package Manager. It comes bundled with recent versions of Python,
+`pip` is the package manager for the Python Package Index. It comes bundled with recent versions of Python,
 otherwise you can find installation instructions [here](https://pip.pypa.io/en/stable/installation/).
 
 You can install MultiQC from [PyPI](https://pypi.python.org/pypi/multiqc) as follows:
@@ -201,9 +299,17 @@ cd MultiQC
 pip install .
 ```
 
+Or, using uv:
+
+```bash
+git clone https://github.com/MultiQC/MultiQC.git
+cd MultiQC
+uv pip install .
+```
+
 This will fetch the latest development code. To update to the latest changes, use `git pull`.
 
-Use the `--editable` flag (`pip install -e .`) if you intend to develop the code locally.
+Use the `--editable` flag (`pip install -e .` or `uv pip install -e .`) if you intend to develop the code locally.
 This symlinks the source files so that you don't have to reinstall every time you edit a file.
 
 `git` not installed? No problem - just download the flat files:

docs/markdown/getting_started/quick_start.md

@@ -9,10 +9,26 @@ This tutorial covers installation and first run for a typical user.
 It's not meant to be comprehensive - see the rest of the documentation for that -
 it's just to get the majority up and running quickly so you can get a taste for how to use MultiQC.
 
-## Install Conda
+## Install MultiQC
+
+### Option A: Using uv (recommended)
+
+[uv](https://docs.astral.sh/uv/) is a fast Python package manager that handles everything — including installing Python for you automatically.
+No need to install Python separately (see [full docs](installation/#uv)).
+
+1. Install uv:
+   ```bash
+   # macOS / Linux
+   curl -LsSf https://astral.sh/uv/install.sh | sh
+   ```
+2. Install MultiQC:
+   ```bash
+   uv tool install multiqc
+   ```
 
-In order to install MultiQC, we first need Python.
-Arguably, the easiest way to do this is with Conda
+### Option B: Using Conda
+
+Alternatively, you can use Conda
 (see [full docs](installation/#python-with-conda)).
 
 1. [Download miniconda](https://conda.io/miniconda.html) for your operating system.
@@ -29,15 +45,12 @@ Arguably, the easiest way to do this is with Conda
    conda create --name myenv python=3.11
    conda activate myenv
    ```
+6. Install MultiQC:
+   ```bash
+   conda install multiqc
+   ```
 
-## Install MultiQC
-
-Now that we have Python, we can install MultiQC.
-As we're already using Conda, we may as well install MultiQC with Conda too (see [full docs](installation/#conda)).
-
-```bash
-conda install multiqc
-```
+### Verify installation
 
 Check that it worked by printing the MultiQC version (or `--help` text):
 
@@ -46,20 +59,20 @@ multiqc --version
 ```
 
 ```txt
-multiqc, version 1.20
+multiqc, version 1.33
 ```
 
 ## Get some example data
 
-To try MultiQC out quickly, you can fetch some example input data from the [Example reports](https://multiqc.info/example-reports/) page.
+To try MultiQC out quickly, you can fetch some example input data from the [Example reports](https://seqera.io/multiqc/#reports) page.
 
 Each example report has a link to _Download input data_.
 You should be able to recreate the example report using this.
 
-For example, for the [RNA-seq report](https://multiqc.info/example-reports/rna-seq/):
+For example, for the [RNA-seq report](https://seqera.io/examples/rna-seq/multiqc_report):
 
 ```bash
-curl -O -J -L http://multiqc.info/examples/rna-seq/data.zip
+curl -O -J -L https://seqera.io/examples/rna-seq/data.zip
 unzip data.zip
 ```
 
@@ -80,7 +93,7 @@ multiqc .
 ```
 
 ```txt
-  /// MultiQC 🔍 | v1.20
+  /// MultiQC 🔍 | v1.33
 
 |           multiqc | Search path : /demo/data
 |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 121/121
@@ -97,7 +110,7 @@ multiqc .
 
 You can see in the log output that MultiQC created a file called `multiqc_report.html`.
 Open it and take a look (you can usually <kbd>ctrl</kbd>/<kbd>cmd</kbd> + click the filename in most terminals).
-It should look basically the same as the example report [on the MultiQC website](https://multiqc.info/example-reports/rna-seq/).
+It should look basically the same as [this example report](https://seqera.io/examples/rna-seq/multiqc_report).
 
 Try using the toolbox features in the right hand sidebar, for example hiding and highlighting specific samples.
 

multiqc/templates/default/compiled/js/multiqc.min.js

@@ -100,6 +100,16 @@ class HeatmapPlot extends Plot {
     let [rows, xcats, ycats] = this.prepData();
     if (rows.length === 0 || xcats.length === 0 || ycats.length === 0) return [];
 
+    // Update layout tick labels to match current (possibly clustered) category order
+    if (this.layout.yaxis.tickmode === "array") {
+      this.layout.yaxis.ticktext = ycats;
+      this.layout.yaxis.tickvals = [...Array(ycats.length).keys()];
+    }
+    if (this.layout.xaxis.tickmode === "array") {
+      this.layout.xaxis.ticktext = xcats;
+      this.layout.xaxis.tickvals = [...Array(xcats.length).keys()];
+    }
+
     if (this.filtYCatsSettings.length > 0) {
       const maxYTicks = (this.layout.height - 200) / 12;
       this.recalculateTicks(this.filtYCatsSettings, this.layout.yaxis, maxYTicks);