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…. for pyodide worker)
* add seqfu stats * Minor fix --------- Co-authored-by: Vlad Savelyev <vladislav.sav@gmail.com>
* WASM workaround: if write_parquet not supported, write csv * Fix * Use debug print
… provided (#3312) * Do not read file if contents exclusion patterns are not provided * Fix tests * Clean config in tests * More cleaning
This adds the pandoc package to the Docker image installation, allowing MultiQC to generate additional output formats when running in Docker containers. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
* Do not read file if contents exclusion patterns are not provided * Optimize for lazy dataframe * Optimize multi-sample runs * Remove try-catches * Use heatmap for FoV plot * Fix * Heatmap: if too wide, determine only width from max_width * Optimizations and feedback * Adjust single-sample plots * Add flat_if_very_large into pconfig * Add helptext * Fix box plot AI summaries * Clean up * Fix FoV heatmap * Use heatmap for both scenarios * Use barplot instead of heatmap * FoV: use red; percentages by default * AI summaries: fix when provider undefined * Fix using default AI provider * OpenAI: default to gpt-5 * Reflect % in max in table * Vertical line positionin * Log scale for distr
* Feedback: rename "detected genes" to "transcript genes", use single threshold line * Unncesessary imports * Box plot: support stats as input instsad of data arrays * Pass stats to box plots * Parse the h5 files for gene counts * Improve transcript quality table * Fix mypy * Fix mypy * Fix mypy * Clean up * Add scanpy dependency * Filter oput low-count cells for nucleus/transcript count ratio and cap plot at 1 * Pass extra legend group and tooltip to linegraph series * Improve Distribution of Transcripts multi-sample plot * Optimized noize threshold calculation
* Fixes * Unique series label for each plot type
When cutadapt processes input from stdin (e.g., /dev/fd/*, -), the original sample name extraction would use these unusable paths as sample names. This fix implements a fallback strategy: 1. Use input paths if they are valid file names (original behavior) 2. Extract sample names from output arguments (--output, --paired-output) when input is from stdin 3. Fall back to JSON filename if other methods fail Fixes cases where stdin input would result in sample names like "/dev/fd/63" instead of meaningful names like "SRR8615409". 🤖 Generated with [Claude Code](https://claude.ai/code) Co-authored-by: Claude <noreply@anthropic.com>
* Bump version * Fix finding repos for current milestone * Changelog * New module docs * Cross-link sample renaming docs (fixes #3316) * Changelog
…issing `scipy` (#3334) * Xenium: warnings about missing scipy * Fix sorting categories * Add scipy dep
* Generate new screengrabs with rich-codex * Fix path --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
… from PdfLatex (#3349) * Update Dockerfile to optionally include all LaTeX requirements. Build two docker images, with and without PDF deps. * Remove duplicate latex margin argument * Shorter easier to read GHA variable names * Docker: simplify CI logic, bump to Python 3.13 * Fix cache cleanup in Dockerfile after Python version bump. Kudos @cursor for spotting that * Update the docs
* "Update Claude PR Assistant workflow" * "Claude Code Review workflow"
Co-authored-by: Josh Chorlton <josh@bugseq.com>
Automation update in script, see #3314 for upstream fixes.
* Fix merge conflicts * Clean up prettier format check from upstream change * Only try to run claude PR reviews when coming from a branch Fails on PRs coming from a fork, as secrets with the API key are not available --------- Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
* add new module som.py * sompy - simplify generate_table_headers() * update happy module description for new sompy module * fix style checks for failing tests * Minor review tweaks * Don't trigger docker build on pyproject.yml This is quite common, as every new module needs it --------- Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
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