Sync with head repo

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

@@ -0,0 +1,51 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Only run on PRs from branches in the same repository (not forks)
+    # This prevents the workflow from failing when secrets aren't available
+    if: github.event.pull_request.head.repo.full_name == github.repository
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+          prompt: |
+            Please review this pull request and provide feedback on:
+            - Code quality and best practices
+            - Potential bugs or issues
+            - Performance considerations
+            - Security concerns
+            - Test coverage
+
+            Use the repository's CLAUDE.md for guidance on style and conventions. Be constructive and helpful in your feedback.
+
+            Use `gh pr comment` with your Bash tool to leave your review as a comment on the PR.
+
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://docs.anthropic.com/en/docs/claude-code/sdk#command-line for available options
+          claude_args: '--allowed-tools "Bash(gh issue view:*),Bash(gh search:*),Bash(gh issue list:*),Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*)"'

.github/workflows/claude.yml

@@ -1,4 +1,4 @@
-name: Claude Code Review
+name: Claude Code
 
 on:
   issue_comment:
@@ -11,28 +11,39 @@ on:
     types: [submitted]
 
 jobs:
-  claude-code-review:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
     runs-on: ubuntu-latest
     permissions:
       contents: read
+      pull-requests: read
       issues: read
-      pull-requests: write
       id-token: write
-
-    if: |
-      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
-      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
-      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
-      (github.event_name == 'issues' && contains(github.event.issue.body, '@claude'))
-
+      actions: read # Required for Claude to read CI results on PRs
     steps:
-      - name: Checkout code
+      - name: Checkout repository
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
-      - name: Run Claude PR Action
-        uses: anthropics/claude-code-action@beta
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
-          timeout_minutes: "60"
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          # Optional: Add claude_args to customize behavior and configuration
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://docs.anthropic.com/en/docs/claude-code/sdk#command-line for available options
+          # claude_args: '--model claude-opus-4-1-20250805 --allowed-tools Bash(gh pr:*)'

.github/workflows/docker.yml

@@ -3,8 +3,8 @@ name: "Docker image"
 on:
   pull_request:
     paths:
-      # Step takes 5 min, too long for PR commits, so leaving it only to significant changes
-      - "pyproject.toml"
+      # Step takes 30 min, too long for PR commits, so leaving it only to significant changes
+      # - "pyproject.toml"
       - "Dockerfile"
   push:
     # Build multiqc:dev on every push to main
@@ -21,6 +21,13 @@ jobs:
   build:
     if: github.repository == 'MultiQC/MultiQC'
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        v:
+          - lab: ""
+            build_args: ""
+          - lab: "pdf-"
+            build_args: "INSTALL_PANDOC=true"
     steps:
       - name: "Check out the repo"
         uses: actions/checkout@v4
@@ -51,29 +58,31 @@ jobs:
 
       - name: "Build dev"
         uses: docker/build-push-action@v3
-        if: github.event_name != 'pull_request' && github.event_name != 'release'
+        if: github.event_name != 'release'
         with:
           # All available with python:3.X-slim are:
           # platforms: linux/386,linux/amd64,linux/arm/v5,linux/arm/v7,linux/arm64/v8,linux/ppc64le,linux/s390x
           # But 32-bit binaries likely require compilation from source so stick with linux/amd64 and linux/arm64 for now
           platforms: linux/amd64,linux/arm64
-          push: true
-          # If it's a PR, use the branch name as a tag, otherwise use "dev"
+          build-args: ${{ matrix.v.build_args }}
+          # Only push if it's commit to main, or workflow_dispatch
+          push: ${{github.event_name != 'pull_request'}}
           tags: |
-            ${{ github.ref == 'refs/heads/main' && 'multiqc/multiqc:dev' || format('multiqc/multiqc:{0}', github.head_ref) }}
-            ${{ github.ref == 'refs/heads/main' && 'ghcr.io/multiqc/multiqc:dev' || format('ghcr.io/multiqc/multiqc:{0}', github.head_ref) }}
+            multiqc/multiqc:${{matrix.v.lab}}dev
+            ghcr.io/multiqc/multiqc:${{matrix.v.lab}}dev
 
       - name: "Build release"
         uses: docker/build-push-action@v3
-        if: github.event_name != 'pull_request' && github.event_name == 'release'
+        if: github.event_name == 'release'
         with:
           # All available with python:3.X-slim are:
           # platforms: linux/386,linux/amd64,linux/arm/v5,linux/arm/v7,linux/arm64/v8,linux/ppc64le,linux/s390x
           # But 32-bit binaries likely require compilation from source so stick with linux/amd64 and linux/arm64 for now
           platforms: linux/amd64,linux/arm64
+          build-args: ${{ matrix.v.build_args }}
           push: true
           tags: |
-            multiqc/multiqc:${{ github.event.release.tag_name }}
-            multiqc/multiqc:latest
-            ghcr.io/multiqc/multiqc:${{ github.event.release.tag_name }}
-            ghcr.io/multiqc/multiqc:latest
+            multiqc/multiqc:${{ matrix.v.lab }}${{ github.event.release.tag_name }}
+            multiqc/multiqc:${{ matrix.v.lab }}latest
+            ghcr.io/multiqc/multiqc:${{ matrix.v.lab }}${{ github.event.release.tag_name }}
+            ghcr.io/multiqc/multiqc:${{ matrix.v.lab }}latest

.gitignore

@@ -59,3 +59,5 @@ package.json
 
 .env
 .claude
+
+Pipfile

CHANGELOG.md

@@ -1,5 +1,56 @@
 # MultiQC Version History
 
+## [MultiQC v1.31](https://github.com/MultiQC/MultiQC/releases/tag/v1.31) - 2025-09-05
+
+Adding new module for [Xenium analysis](https://www.10xgenomics.com/products/xenium-analysis), 10x Genomics Xenium spatial transcriptomics quality control report.
+
+The parquet format is stable since 1.29, renaming the output file from `BETA-multiqc.parquet` to `multiqc.parquet`.
+
+### New modules
+
+- Xenium QC ([#3276](https://github.com/MultiQC/MultiQC/pull/3276), [#3313](https://github.com/MultiQC/MultiQC/pull/3313), [#3323](https://github.com/MultiQC/MultiQC/pull/3323))
+- Seqfu: `stats` command - FASTA/FASTQ files stats ([#3271](https://github.com/MultiQC/MultiQC/pull/3271))
+
+### Feature updates and improvements
+
+- Add `return_html` parameter for programmatic HTML access ([#3304](https://github.com/MultiQC/MultiQC/pull/3304))
+- File search optimization: avoid reading files when contents exclusion patterns are not
+  provided ([#3312](https://github.com/MultiQC/MultiQC/pull/3312))
+- Rename `BETA-multiqc.parquet` to `multiqc.parquet` ([#3332](https://github.com/MultiQC/MultiQC/pull/3332))
+
+### Fixes
+
+- Scatter plot: fix hiding dots by legend click ([#3321](https://github.com/MultiQC/MultiQC/pull/3321))
+- Plots: set unique series label for each plot type ([#3330](https://github.com/MultiQC/MultiQC/pull/3330))
+- Fix bulk sample renaming buttons ([#3300](https://github.com/MultiQC/MultiQC/pull/3300))
+- Fix config flag types in schema ([#3318](https://github.com/MultiQC/MultiQC/pull/3318))
+- Ignore pyc files when copying html files ([#3320](https://github.com/MultiQC/MultiQC/pull/3320))
+
+### Module updates
+
+- Picard tools: enhance QualityByCycleMetrics to support original quality scores ([#3307](https://github.com/MultiQC/MultiQC/pull/3307))
+- STAR: improve module color scheme for better accessibility ([#3305](https://github.com/MultiQC/MultiQC/pull/3305), [#3306](https://github.com/MultiQC/MultiQC/pull/3306))
+- Sequali: support insert size metrics ([#3303](https://github.com/MultiQC/MultiQC/pull/3303))
+- Missing modules to general stats: Busco, CheckM, CheckM2, GTDB-Tk ([#3289](https://github.com/MultiQC/MultiQC/pull/3289))
+- cells2stats: add support for optical pooled screening output ([#3277](https://github.com/MultiQC/MultiQC/pull/3277))
+- fastp: add before-filtering mean r1/r2 length to general stats ([#3280](https://github.com/MultiQC/MultiQC/pull/3280))
+- Cutadapt: improve sample name extraction for stdin input ([#3333](https://github.com/MultiQC/MultiQC/pull/3333))
+
+### Module fixes
+
+- bases2fastq: fix index error ([#3328](https://github.com/MultiQC/MultiQC/pull/3328))
+- Picard: fix VariantCallingMetrics to support sample renaming ([#3298](https://github.com/MultiQC/MultiQC/pull/3298))
+- fastp: fix sample naming for paired-end reads ([#3302](https://github.com/MultiQC/MultiQC/pull/3302))
+- bcftools: fix singleton count calculation to include indels ([#3295](https://github.com/MultiQC/MultiQC/pull/3295))
+- CheckM2: column spelling fix ([#3283](https://github.com/MultiQC/MultiQC/pull/3283))
+- Bulk replace deprecated `hide_empty` with `hide_zero_cats` ([#3296](https://github.com/MultiQC/MultiQC/pull/3296))
+
+### Infrastructure and packaging
+
+- WASM workaround: if `write_parquet` not supported by polars, write a CSV file ([#3309](https://github.com/MultiQC/MultiQC/pull/3309))
+- Add Claude instructions ([#3301](https://github.com/MultiQC/MultiQC/pull/3301))
+- Add Claude review action ([#3299](https://github.com/MultiQC/MultiQC/pull/3299))
+
 ## [MultiQC v1.30](https://github.com/MultiQC/MultiQC/releases/tag/v1.30) - 2025-07-09
 
 Minor improvements and fixes.

CLAUDE.md

@@ -1,5 +1,9 @@
 # CLAUDE.md
 
+# IMPORTANT
+
+Never push to main branch. When asked to add a change or create a pull request, always check if we are on main first. If we are, create a new branch and push to it.
+
 This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 
 ## Development Commands

Dockerfile

@@ -1,9 +1,12 @@
-FROM python:3.12-slim
+FROM python:3.13-slim
 
 LABEL author="Phil Ewels & Vlad Savelyev" \
       description="MultiQC" \
       maintainer="phil.ewels@seqera.io"
 
+# Optional pandoc installation for PDF support
+ARG INSTALL_PANDOC=false
+
 RUN mkdir /usr/src/multiqc
 
 # Add the MultiQC source files to the container
@@ -28,6 +31,10 @@ RUN \
     && \
     echo "Docker build log: Install procps" 1>&2 && \
     apt-get install -y -qq procps && \
+    if [ "$INSTALL_PANDOC" = "true" ]; then \
+        echo "Docker build log: Install pandoc and LaTeX for PDF generation" 1>&2 && \
+        apt-get install -y -qq pandoc texlive-latex-base texlive-fonts-recommended texlive-latex-extra texlive-luatex; \
+    fi && \
     echo "Docker build log: Clean apt cache" 1>&2 && \
     rm -rf /var/lib/apt/lists/* && \
     apt-get clean -y && \
@@ -37,7 +44,7 @@ RUN \
     # Install MultiQC
     pip install --verbose --no-cache-dir /usr/src/multiqc && \
     echo "Docker build log: Delete python cache directories" 1>&2 && \
-    find /usr/local/lib/python3.12 \( -iname '*.c' -o -iname '*.pxd' -o -iname '*.pyd' -o -iname '__pycache__' \) -printf "\"%p\" " | \
+    find /usr/local/lib/python3.13 \( -iname '*.c' -o -iname '*.pxd' -o -iname '*.pyd' -o -iname '__pycache__' \) -printf "\"%p\" " | \
     xargs rm -rf {} && \
     echo "Docker build log: Delete /usr/src/multiqc" 1>&2 && \
     rm -rf "/usr/src/multiqc/" && \
@@ -53,7 +60,7 @@ WORKDIR /home/multiqc
 
 # Check everything is working smoothly
 RUN echo "Docker build log: Testing multiqc" 1>&2 && \
-    multiqc --help 
+    multiqc --help
 
 # Display the command line help if the container is run without any parameters
-CMD multiqc --help
+CMD multiqc --help