UMI-tools: support extract command
#2296
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vladsavelyev
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vladsavelyev
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Feb 23, 2024
* UMI-tools: support extract command * [automated] Update CHANGELOG.md * Add barplot * Barplot with extract stats * Doc * Changelog * Lint * Fix duplicated IDs in linting * Merge conflict --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
ewels
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Feb 24, 2024
* Rewrite version checker to use new API endpoint * Move version_check_url into the config, for local testing * Version check URL * Clean up * Typo * Parse CI env var * Fix * Catch timeout error * UMI-tools: support `extract` command (#2296) * UMI-tools: support extract command * [automated] Update CHANGELOG.md * Add barplot * Barplot with extract stats * Doc * Changelog * Lint * Fix duplicated IDs in linting * Merge conflict --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * Infinite dmax or dmin fail JSON dump load in JavaScript (#2354) * Infinite dmax or dmin fail JSON dump load in JavaScript * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * Fix changelog.py for module updates * Whatshap: robust to stdout appended to TSV (#2361) * Drop `full_figure_for_development` the call to avoid Kaleido issues (#2359) * Wrap `full_figure_for_development` in try-except to handle Kaleido errors * [automated] Update CHANGELOG.md * Get around read-only /tmp * Remove the full_figure_for_development call for good, just re-calcualte range from data * Changelog * Comments --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * PURPLE: support v4.0.1 output without `version` column (#2366) * Purple: support v4.0.1 output without version column * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * Ignore `.parquet` files. More robust `htseq` file reading loop (#2364) * Ignore .parquet files. Handle htseq unicode errors * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * Add box plot (#2358) * Add box plot * [automated] Update CHANGELOG.md * Fix linting * CSP * Fix sample order * Allow overriding title for a dataset tab * Violin: color dots blue in monochrome violins to indiciate interactivity * Mono color for boxes, support highliting * Rename beeswarm to violin * Barplot: stacking: normal should mean stacked, not grouped * Update plotting documentation * Docs * Redirect beeswarm * CSP * Update the flat plot section and remove highcharts mention --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * Replace `setup.py` with `pyproject.toml` (#2353) * Replace setup.py with pyproject.toml * [automated] Update CHANGELOG.md * Add myself as author --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * Put matplotlib back into main deps (#2370) * Put matplotlib back into main deps * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> * Generic font family for Plotly (#2368) * Generic font family for Plotly * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * Samtools `coverage` submodule (#2356) * Allow override title per-dataset * Add samtools coverage submodule * [automated] Update CHANGELOG.md * Fix changelog * Update multiqc/modules/samtools/rmdup.py Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * Fix rmdup regex --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * Update `modules.md`: `pyproject.toml`, `"shared_key": "read_count"`, ruffify (#2371) * Update modules.md: `pyproject.toml`, `"shared_key": "read_count"`, ruffify * [automated] Update CHANGELOG.md * Apply suggestions from code review --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io> --------- Co-authored-by: Vlad Savelyev <vladislav.sav@gmail.com> Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
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Adds a new subcommand
extract, so now bothdedupandextractare supported. Adds a general stats column fro the number of extracted reads, as well as a bar plot showing the split between regex matches.Fix #2284